[Bioc-devel] Better late than never.... NEWS
James MacDonald
jmacdon at med.umich.edu
Mon Oct 15 17:49:49 CEST 2007
August - September 2007
ABarray
* : Added parameter for none normalization.
aCGH
* : Bumped for LazyLoad.
ACME
* : 1.3.2
=====
* Major changes to class structures. Now based on
ExpressionSets.
* Still needs some significant cleanup of other functions,
but
classes seem to
work as does do.aGFF.calc
* : * fixed write.sgr and started working on plot functions
again.
* : not quite there yet
* : 1.3.0
=====
This backs out all the new changes since last release to fix
up
things for new release.
adSplit
* : Bumped for LazyLoad.
affxparser
* : Committing in for backup. Will commit the DESCRIPTION with
increased version number later when I know then new stuff
works.
I am running tons of redundancy testing on it right now using
aroma.affymetrix.
* : OK, updating the devel version of affxparser to v1.9.3
(from
v1.9.2). For the actual updates, see the release version
v1.8.3,
because that contains the same updates.
Version: 1.9.3 [2007-08-16]
o See updated made to release v1.8.3 below.
o The only difference between v1.9.3 and v1.8.3 is the
modification
of findCfd() in v1.9.2.
Version: 1.9.2 [2007-07-27]
o This BioC devel version requires R v2.6.0 due to a change
of
how strings are handled in C by BioC.
o Modified findCdf() such that it is possible to set an
alternative
function for how CDFs are located.
* : Updated to Fusion 1.0.9 and bumped the version number. I
also
decreased the dependency to R (>= 2.5.0), simply because I
don't
knwo if we need this...
* : Only comments for now, version is still to be bumped, which
will not happen before new AffymetrixDataTestFiles package is
on
BioC.
o Added argument 'recursive=TRUE' to findCdf(). Note, the
current
working directory is always scanned first, but never
recursively
(unless explicitly added to the search path). This is to
avoid
endless scans in case the search path has not been set.
o findFiles() now do a breath-first search in lexicographic
order.
o Removed default search paths cdf/ and data/cdf/. We do not
want
to enforce a standard path.
o Now the examples (as well as test scripts) utilize data
available
in the new Bioconductor AffymetrixDataTestFiles package. This
means that R CMD check now runs much more tests, which is
good.
o CLEAN UP: Removed many of the old testscripts/ scripts.
They
are now under tests/.
o BUG FIX: If the destination file already existed,
convertCel()
would
correctly detect that, but would give the name of the source
file.
* : The recent updates to findFiles() did not handle filename
patterns correctly.
* : Bumped affxparser (devel) to the following version:
Version: 1.9.5 [2007-09-16]
o Added argument 'recursive=TRUE' to findCdf(). Note, the
current
working directory is always scanned first, but never
recursively
(unless explicitly added to the search path). This is to
avoid
"endless" scans in case the search path has not been set.
o findFiles() now do a breath-first search in lexicographic
order.
o Removed default search paths cdf/ and data/cdf/. We do not
want
to enforce a standard path.
o Now the examples (as well as test scripts) utilize data
available
in the new Bioconductor AffymetrixDataTestFiles package. This
means that R CMD check now runs much more tests, which is
good.
o CLEAN UP: Removed many of the old testscripts/ scripts.
They
are now under tests/.
o BUG FIX: findFiles() was not robust against broken Unix
links.
o BUG FIX: If the destination file already existed,
convertCel()
would
correctly detect that, but would report the name of the
source
file.
affy
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
* : small vignette correction
* : fix in computeExprSet (trouble with named ids,
mostly an S4 thing)
bumped version number
* : - fixed geneNames to featureNames (spotted by Robert -
presumably
missing in the move to ExpressionSet)
- bumped version number
* : added citation
* : Fixing ppsetApply example
affycomp
* : Fix bracket pairs in Rd
* : Add Suggests splines to remove warning.
affycoretools
* : Use require, not library to load optional packages in code
* : Backed out xlsReadWrite stuff and made some other changes.
* : Changes to package structure and vignettes to allow package
to
pass R CMD check.
* : Kludgy fix in linksBM() to account for the fact that
Ensembl
uses different filter and attribute names for the HG_U133av2
chip. Also adjusted the default 'annot' argument to
probes2table() to match limma2annaffy() and vennSelect(),
which
were previously modified because the output of aaf.handler()
changed.:
AffyExpress
* : added the AffyExpress package
Maintainer: Xuejun Arthur Li
affyio
* : fix for read_bpmap
* : fix problem with too many file handles left open problem
for
binary CEL files
* : Fix crash in affyio due to extra call to fclose
Also updating required version for oligo
* : add support for reading command console (aka generic)
format
cel files
Also will read gzipped versions of the same.
* : fix some small compiler warnings
* : fix uninitialized variable warning.
affylmGUI
* : Version 1.11.5 now displays Citation information in a GUI
Message Box as well as in the R Console.
* : minor code formatting changes and remove INDEX file from
source
tree
* : affylmGUI version 1.11.6. htmlReport now uses parameters set
in
the topTable process.
main.R and htmlReport.R code reformatted to suit me.
affyPLM
* : move affydata from "depends" to "suggests"
* : fix vignettes for dealing with "Dilution" dataset from
affydata
* : more "R_rlm_interfaces.c" from affyPLM to preprocessCore
* : fix some compiler warnings
* : clean up include files. Try to differentiate similar named
c
source code files in affyPLM and preprocessCore by renaming
these
files PLM_*
* : restructed medianPM and median_logPM code
* : commit the deletion and addition of a file (should have
been
previously committed)
* : small doc fix
* : Add Sys.sleep in MAplots.Rnw, to give ghostscript on Windows
a
few seconds to finish before Sweave removes necessary
temporary
files
* : resync affyPLM with changes in preprocessCore
affyQCReport
* : added \usepackage{underscore} on user request - let's see if
it
breaks anything
* : minor addition of additional latex package dependency
altcdfenvs
* : - cut out dependency to splicegear
- fixes in the documentation
* : - Fixes an unmatched "}"
- Bumped version number
annaffy
* : Fixed problem with primitive methods not dispatching for
annaffy S4 objects
Removed all dependencies on non-db hgu95av2
Renamed "LocusLink" to "Gene" in aaf.handler()
Updated aafLocusLink URL
Updated aafCytoband URL
aafCytoband now uses Gene ID instead of Accession Number for
lookup
Updated aafGOItem URL to show detail view on AmiGO
* : Remove classes and functions related to SUMFUNC maps
THe SUMFUNC annotation map was never properly implemented and
has
been
removed from the annotation data packages that are candidates
for
the
next release.
* : Forgot to change some hgu95av2 require() lines in the
examples
* : Quick fix for is_dbpackage internal helper function
This function or similar should be in the AnnotationDbi
package.
This
is a quick fix to get things going. Thanks to Jim MacDonald
for
the
bug report.
* : Fixed is_dbpackage() to deal with recent db_conn changes in
the
ann db packages. Version bump.
* : one more try
* : even better (+ small reorganizing)
* : Small change in getHTML() to remove warnings that didn't
affect
the output.
AnnBuilder
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
* : Fixed a small problem where a list was expected.
List was not always being returned from function
getList4GO() So switched sapply() to an lapply().
* : Passed check under R-2.6.0
* : Use the Artistic License instead of LGPL as default license
* : Switch to Artistic
* : we need to move much of the orgName stuff to annotate, since
it
is used
there and the package dependencies go from there to here
* : modified man page accordingly
* : removed one more arg
* : Added dire warning to users of this function.
annotate
* : use featureNames rather than geneNames accessor
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
* : Fix useProbeInfo.Rnw
It needed to load the annotate package. There is also a
problem
with
Biostrings::nchar when given an empty view. This patch works
around
the error by calling length instead.
* : Allow getAnnMap to understand "foo" and "foo.db" as chip
name
* : Remove defunct function installDataPackage
* : Teach lookUp to use getAnnMap
This makes lookUp flexible enough for use with env and SQLite
based
annotation data packages.
* : Remove doc for removed function
* : fix doc for lookUp
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : GOTerms class moved to AnnotationDbi, GONode removed
In order for GO and GO.db packages to be used interchangeably
and
for
function in the annotate package to function properly, we
must
have a
single shared class representing GO terms. This patch moves
the
GOTerms class definition to AnnotationDbi and removes
references
to
the GONode class which was intended as a replacement.
* : buildChromLocation now uses getAnnMap and is db ann pkg
compatible
* : getAnnMap now uses inherits=FALSE in interal get call for
safety
* : DB compatibility fixes for chromLocation class
Changed slot types for probesToChrom and geneSymbols from
environment
to ANY since these need to be able to hold AnnotationDbi
objects
when
using db-based ann pkgs. A class union might be a possible
solution,
but I'm concerned about possible dispatch issues that such a
union
might introduce.
* : Remove commented code for cleanup
* : ACCNUMStats now uses getAnnMap
* : use annotation() accessor instead of slot access
* : No need to require annotate in the annotate package.
* : probesByLL uses getAnnMap
* : Version bump, use standard license
* : expand doc for getAnnMap
* : Fixes made to htmlpage() to use xtable() instead of
building
the table by hand. Also made changes to man pages and
prettyOutput vignette for clarity.
* : More refactoring to htmlpage() to ensure correct handling
of
input.
* : moving a few pieces of code around so that we don't have
undefined globals
* : one more global squashed
* : fixed a typo in a warning
* : found lots of references to exprSet, geneNames etc -
not sure why these did not cause build warnings
* : removed reference to exprSet from comment
* : fixed typos and removed LocusLinks
AnnotationDbi
* : Started the flatten.R file where all code related to
flattening
maps (db-based and environments) will go.
* : cosmetic
* : Documentation for new ALIAS maps.
This adds documentation for the newly
added alias maps. The documentation for
ALIAS2EG should also be applicable for the
HUMAN.DB and RODENT.DB packates.
* : Update for manual files on the ALIAS mappings.
This just adds a note to these man pages to
indicate that in fact we mean to represent ALL
the possible gene symbols in this mapping,
including those already listed in the symbol
map.
* : When building an ann db pkg, the user has now full control
on
the Title that goes into the DESCRIPTION file. Used this new
feature in the master index file to set a customized title
for
some of the custom array pkgs. Some more tweaks to
R/flatten.R.
Version bump.
* : small update in the master index file
* : small fix in AnnDbPkgSeed class definition
* : some improvements to various non-chip based pkg templates +
some reorganization and updates to the master index file
* : Added the definition of 2 new maps: ALIAS2PROBE in
createAnnObjs.HUMANCHIP_DB() and ALIAS2EG in
createAnnObjs.HUMAN_DB().
* : Removed broken "initialize" method for AnnDbPkgSeed objects
(not needed anymore).
* : fixed some typos and inaccuracies in various template man
pages
* : small fixes and improvements in
getSymbolValuesForManPages()
* : forgot to add ALIAS2PROBE map to the list of predefined maps
in
createAnnObjs.HUMANCHIP_DB()
* : createMAPCOUNTS() now generates a MAPCOUNTS map where the
map
names are in alphabetical order
* : Adds documentation for the RODENT EG pkgs.
This adds documentation for the rodent EG
pkgs. This should be the same as the documentation
for the human pkgs. Except for the OMIM which
I see has snuck in here and will be subsequently
removed...
* : This adds documentation for the human EG pkgs.
This documentation is largely redundant with the
Rodent documentation. there are only a few minor
differences (OMIM). I am going to discuss this
with Herve since this is a bad thing.
* : Removes bad/uneeded documentation files.
As promised, this removes the unwanted OMIM doc
and other documentation from the repository.
* : Corrected misunderstanding about naming.
This corrects a misunderstanding that I had
about how we were going to name things in the
EG packages. Next I will correct this mistake
for the rodent packages.
* : Correct misunderstanding in pkg names.
this just corrects a misunderstanding in the
way that the maps should be named for the
rodent EG packages. We want to use 'EG' instead
of 'ENTREZID'
* : Added the no.docs arg to the "makeAnnDbPkg" generic.
* : Better name it no.man instead of no.docs. Updated the man
page
for makeAnnDbPkg().
* : added new portable (and commented) HUMANCHIP_DB schema
under
inst/extdata/
* : Added the index creation to HUMANCHIP_DB.sql. Added
RODENTCHIP_DB.sql
* : centralized general comments about the schemas in
DBschemas-README.TXT
* : Added HUMAN_DB.sql
* : added RODENT_DB.sql
* : Corrected a bug in the way these man pages reference ea.
other.
This just fixes some bugs that were holdovers from the
initial
grotesque copy paste that was done with these man files
(since
they
really should be nearly identical to the chip based ones...)
* : Moved man pages for reverse maps into same documents as
forward.
This will hopefully help to make things more manageable. I
will
document all future reverse maps along with the forward maps.
* : More merges in the man pages.
This just merges one more man page that I missed earlier and
fixes a
couple of documentation errors.
* : Added man page entries for reverse maps where appropriate.
For each possible reverse map I have added a man page entry.
* : Respect ifnotfound=NA in mget
This patch allows users to specify ifnotfound=NA in calls to
mget.
The support for ifnotfound is minimal. Only '=NA' is
supported,
but
this is the common use case we see in existing code.
* : deal properly with _any_ possible 'ifnotfound' value
provided
by the user
* : added GO_DB.sql (is not ready yet, there is actually much
more
ugliness/breakage in our current GO schema than I imagined)
* : Move in-development schemas to extdata/schema_next
extdata/schema will soon hold _the_ current version of the
annotation
data package schemas. extdata/schema_next is a place for in
progress
updates and changes.
* : new GO_DB.sql is ready (tested with SQLite and PostgreSQL)
* : added KEGG_DB.sql
* : commented data columns with their "real world types" in
HUMANCHIP_DB.sql and RODENTCHIP_DB.sql
* : commented data columns with their "real world types" in
HUMAN_DB.sql and RODENT_DB.sql
* : Renamed folders: schema_next -> schemas_1.0, schema ->
schemas_tmp. Started to put degraded version of the 1.0
schemas
under schemas_tmp/
* : cosmetic
* : Added more "degraded" versions of the 1.0 schemas under
schemas_tmp/
* : 1 more degraded schema
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : started using portable FOREIGN KEY syntax (compatible with
MySQL+InnoDB and PostgreSQL)
* : more schemas with portable FOREIGN KEY syntax (compatible
with
MySQL+InnoDB and PostgreSQL)
* : more schemas with portable FOREIGN KEY syntax (compatible
with
MySQL+InnoDB and PostgreSQL)
* : added new real world type "sequence name" (SQL type:
VARCHAR(20)) and use it in the "chromosome_locations" tables
* : small update
* : removed the "accessions" table from the HUMANCHIP_DB and
RODENTCHIP_DB schemas
* : renamed schemas_tmp/ -> schemas_0.9/
* : all schemas now use portable FOREIGN KEY syntax (compatible
with MySQL+InnoDB and PostgreSQL)
* : added KEGG_DB.sql to schemas_0.9/
* : added inst/DBschemas/ folder where all the schema related
stuff
that is currently under inst/extdata/ will go
* : moved all schema related stuff to the new place
* : added SchemaGuidelines.txt
* : added DataTypes.txt to schemas_0.9/ and schemas_1.0/
* : renamed README.TXT file -> 00README.TXT under schemas_0.9/
and
schemas_1.0/ and updated them
* : one more column renamed (disruptive change) in schemas_1.0
* : started adding YEAST_DB.sql to schemas_0.9/
* : Added YEAST_DB.sql to schemas_0.9/ (DataTypes comments not
ready yet). Some cosmetic polishing to many schemas.
* : cosmetic
* : version bump
* : Add make_eg_to_go_map helper function
When dealing with chip packages programatically, we often need
to
map
Entrez to GO and the reverse. This patch provides two helper
functions to achieve this. When map pluggability comes
online,
these
functions can go away. This is a *temporary* solution.
* : Added data types used in YEAST_DB to DataTypes.txt.
Commented
data column definitions in YEAST_DB.sql with their "real
world
types" (aka "external data types").
* : Added YEASTCHIP_DB.sql to schemas_0.9/
* : small update
* : Added ARABIDOPSISCHIP_DB.sql to schemas_0.9/
* : Replaced the "names" methods for AnnDbMap objects by the
"keys"
methods (new generic). Made all the renaming that this change
implies. Still need some testing before version bump.
* : Tested the "names"-to-"keys" changes. Found some minor
problems. Fixed them. Version bump.
* : Another difference with the other chip-based schemas:
probes.probe_id can't be a PRIMARY KEY for ARABIDOPSISCHIP_DB
(it
is not unique i.e. the same probe id can be linked to several
AGI
locus IDs.
* : Started to implement the new "AnnDbBimap" class and
subclasses
+ some preliminary rework needed in R/FlatBimap.R. Package
will
be temporarily broken.
* : Migrated most AtomicAnnDbMap predefined objects to the new
AtomicAnnDbBimap class. Package should work again but
migration
needs to be completed before version bump.
* : End of migration from AnnDbMap to AnnDbBimap. Still need
some
testing/troubleshooting (vignette does not build). Version
bump
anyway.
* : renamed AnnDbMap-envirAPI.R -> AnnDbBimap-envirAPI.R
* : Fix AnnDbMapDemo.Rnw: we were feeding NA as a key
* : - Added support for new FLYCHIP_DB schema.
- Updated ANNDBPKG-INDEX.TXT with entries for the 3 new fly
chip
db packages.
- Fixed small bugs in the template man pages (introduced by
recent change of
signature of the as.list method for AnnDbBimap objects).
- Version bump from 0.0.94 to 0.1.0
* : - Added map subsetting methods "left.keys<-" and
"right.keys<-"
(now the
"subset" method is just a convenient wrapper that allows
subsetting
of the left and right keys in a single operation).
- The "show" method for AnnDbBimap objects now makes the
difference between
a map and a submap (a submap being the result of subsetting a
map).
- Fixed a few methods that were broken for submap objects
("nrow",
and the "*.mappedKeys" methods).
- Some improvements to the SQL query caching mechanism.
- Some simplification and cleaning in many places.
- Version bump.
* : - Renamed BimapAPI0 interface -> Bimap
- Added the "keys<-" method.
- Moved strictly Bimap stuff from FlatBimap.R to new Bimap.R
file.
- Started to document the Bimap interface.
* : more fixes, cleaning and documentation
* : one less warning
* : Lots of renaming (methods and class slots). In particular,
all
left/right
methods now have "L" or "R" in their name instead of "left"
or
"right".
Overall naming is more consistent, readable and convenient
(names
are
shorter). Version bump.
* : cosmetic
* : more renaming: L2Rpath -> L2Rchain, L2Rbrick -> L2Rlink
* : - Some internal changes and improvements (clear distinction
between tags and
attribs).
- Improved show method for Bimap objects.
- Version bump.
* : - renamed Lcolname -> Lkeyname, Rcolname -> Rkeyname,
Tcolname
-> tagname
and Rattrib_colnames -> Rattribnames
- fixed bug in initialize method for FlatBimap
- fixed bug in flatten (still doesn't work for Go3AnnDbBimap)
* : renamed Rattrib_colname -> Rattribname and collabels ->
colmetanames
* : - Renamed Lkeyname/Rkeyname slots for class L2Rlink ->
Lcolname/Rcolname.
- Fixed bug in makeGo3L2Rchain() that was breaking the
Go3AnnDbBimap
objects.
- Fixed and improved .makeSQLchunks().
- Version bump.
* : depends on RSQLite >= 0.5-6
* : ARABIDOPSISCHIP_DB schema:
- renamed current ENZYME map -> ARACYCENZYME (probes to
AraCyc
enzyme names
mapping)
- replaced data currently in ENZYME map by probes to EC
numbers
mapping
Version bump.
* : HUMAN_DB and RODENT_DB schema:
- removed GENENAME2EG amp (as suggested by Marc)
ARABIDOPSISCHIP_DB schema (from last commit):
- removed ENTREZID map (was an alias for the ACCNUM map, which
is
a mapping
between probes and AGI locus IDs)
* : - Added support for FLY_DB schema.
- Updated master index ANNDBPKG-INDEX.TXT.
- Version bump.
* : tolerate missing manufacturerUrl when making a .db pkg
* : with a warning
* : YEAST_DB schema:
- Renamed *2PROBE maps -> *2SGD
- Removed GO2ALLPROBES map
* : - Moved master index ANNDBPKG-INDEX.TXT from inst/extdata/
to
inst/extdata/GentlemanLab/
- Added batch-script.R to inst/extdata/GentlemanLab/
* : - added [ operator for Bimap objects
- fixed the links/count.links methods for AnnDbBimap objects
(still
needs some testing)
- fixed problem with NULL data frames with 0 rows that was
affecting
code like mget("all", GOBPPARENTS, ifnotfound=NA) (found in
GOstats)
- version bumped
* : Replaced previous dirty fix for "NULL data frames with 0
rows"
problem
with cleaner fix.
Version bump.
* : - Changed semantic of colmetanames().
- Replaced flatten arg 'with.Rattribs' by 'drop.Rattribs'.
- Fixed bug in flatten method for Go3AnnDbBimap objects.
* : FLYCHIP_DB/FLY_DB schemas: renamed FB_id -> flybase_id
* : simplified the compareAnnDataIn2Pkgs() framework
* : renamed links() -> edges(), count.links() -> count.edges()
* : clean up
* : - added "Rattribnames<-" for Bimap objects
- version bump
* : bumped all db packages versions from *.99.0 to *.99.1 in
the
master index file
* : renamed edges() -> links(), count.edges() -> count.links()
(back to their original names, because of a conflict with the
"edge" generic in the graph package). version bump.
* : added TODO.TXT file
* : - map[["invalidkey"]] now returns NULL (at the cost of a
performance
penalty)
- small bug fixes
* : added man page for environment-like API
* : - polishing the "ls" method
- small fix to the "eapply" method
- added a "sample" method for environments in addition to the
method for AnnDbBimap objects
* : added (empty) man page for AnnDbBimap objects
* : - start new man page for Bimap methods (other than key
methods)
- suppressed a few warnings
* : - next .db roaster will have "The Artistic License, Version
2.0" (on Robert's
request)
- version bump
* : - No more attempt to define "is.na" methods for my objects
(the
semantic
of "is.na" for environments does not align with what I would
expect,
looks like a silly semantic to me anyway). So added new
"isNA"
generic
with methods for Bimap, environment and ANY objects (for
ANYi,
it's just
an alias for "is.na").
- More doc.
- Version bump.
* : GOTerms class moved to AnnotationDbi, GONode removed
In order for GO and GO.db packages to be used interchangeably
and
for
function in the annotate package to function properly, we
must
have a
single shared class representing GO terms. This patch moves
the
GOTerms class definition to AnnotationDbi and removes
references
to
the GONode class which was intended as a replacement.
* : Fix makeAnnDbPkg so that dirs are created before file.copy
is
called.
This patch makes the dest location more explicit rather than
relying
on the (empty) template dir.
* : Fix the dir creation fix. Must not error out if it already
exists
* : Changes to support legacy version of YEAST.
These changes are only here to just support the old YEAST
package
so
that it can be "spoofed" to a classic format.
* : Call paste one less time to speed up .toSQLStringSet
sep and collapse can occur in a single paste call. For long
vectors
this is about 2x faster than two calls to paste.
* : Add toSQLStringSet exported helper function
Since users cannot use sQuote for building SQL, we export a
helper
function for building SQL value lists.
* : Remove bad constraint from probes table on chip packages
This change only affects packages for rodents and humans. It
drops
the not null constraint from the accessions collumn which is
problematic since lousy platforms will sometimes have probes
that
are
measuring "who-knows what". Users ought to have a right to
know
when
they are using a probe like this...
* : also removed NOT NULL constraint on probes.accession column
in
schemas_1.0/HUMANCHIP_DB.sql and
schemas_1.0/RODENTCHIP_DB.sql
(replaced NOT NULL by NULL)
* : Updated dual man pages for Enzyme and GO.
This just updates these two man pages so that they are no
longer
broken.
* : added FLYCHIP_DB and FLY_DB schema definitions (version
0.9)
* : Man page updates for EG style packages.
These updates make corrections to the double man pages in the
EG
style
packages.
* : Fixed error in ACCNUM and Added page for Flybase IDs.
This just corrects a typo in the ACCNUM page and adds a man
page
for
the new Flybase Map.
* : Adds FLYBASE man page for fly chip based packages.
This just adds a flybase man page to the fly chip based
packages.
Note that for these packages, the man page should NOT contain
a
reverse map since there is no reverse map planned for this
package.
* : Update CHRLOC to make the env less confusing.
This just adds a sentence to the description of this
environment
so
that users will be less confused about what the data
represents.
* : Adds raw documentation for the YEAST package.
These files still need to be gone through and modified to
make
them
accurate, but these will be the man pages for this package.
* : Removed unwanted man pages from this repository.
* : Updates directions for some of the man pages.
This updates man pages for a number of the YEAST.DB man
pages.
* : More updates to the YEAST Man pages.
It has now been decided that the "2SGD" maps will become
"2ORF"
maps
this is to prevent future confusion with SGD systematic IDs
which
are
different from the classic ORF IDs that the YEAST package has
always
used.
* : This completes the addition of the man pages.
This completes the addition of the man pages for the
org.Sc.sgd.db
package. (aka as the revamped YEAST package)
* : This updates the rest of the double man pages in the EG
based
packages.
The EG based packages had to be rearranged to reduce the
duplication
and this change does that.
* : - YEAST_DB schema: Renamed *2SGD maps -> *2ORF
- Updated Version entries in GentlemanLab master index file
in
order to produce
the *.99.3 roaster
- Version bumped to 0.99.0 (we're getting close!)
* : This updates the man pages for REFSEQ
The REFSEQ pages were still inelegantly doubled up for
FLY.DB,
HUMAN.DB and RODENT.DB. This fixes that.
* : - Renamed db_file -> @ANNOBJPREFIX at _dbfile in all package
templates.
- Renamed db_conn -> @ANNOBJPREFIX at _dbconn in all package
templates and made
it a function instead of just a variable.
- Modified man page templates consequently.
- Version bump.
* : Replaces COMMON2SYSTEMATIC man page with COMMON2ORF.
* : Improved Title and Description in organised-based package
templates.
* : YEAST_DB schema: renamed COMMON2SYSTEMATIC map ->
COMMON2ORF.
* : small update to our in-house batch script
* : small fix
* : ARABIDOPSISCHIP.DB template: removed man page for ENTREZID
map.
Version bump.
* : Added man page for ARACYCENZYME.
This just adds a man page for the new ARACYCENZYME map.
* : Adds man pages for GO2ORF and GO2ALLORFs for org.Sc.sgd.db
* : Added man pages for GO2EG and GO2ALLEG to organism pkgs
Added for FLY.DB, RODENT.DB and HUMAN.DB
* : oops, small bug in the vignette
* : Removed these man pages since they are covered already
These man pages are already covered by double man pages GO.Rd
in
each
of the organism based packges.
* : fixed problem in make_eg_to_go_map() introduced by recent
replacement (and renaming) of db_conn by a function
* : - HUMAN, RODENT and FLY schemas: added support for the
GO2ALLEGS map
- YEAST schema: added support for the GO2ALLORFS map
- modified schemas definitions (0.9 and 0.1) consequently
- version bump
* : bumped db roaster from .99.3 to .99.4 in master index file
used
at the Gentleman Lab
* : Added new Package for Robert.
This just adds an entry to the shared file so that
AnnotationDbi
can
make the new annotation package that Robert has requested.
* : Bug fixes in GO2ALL man pages
This just fixes some typos in these man pages.
* : Edit for Roberts Ovarian cancer package.
* : - Replaced "mappedkeys" method for "ANY" by 2 methods: 1
for
"environment"
and 1 for "vector" (it doesn't seem to make sense to try to
support more
than that).
- Small fix in "mappedkeys" methods for "environment" and
"vector" when the
argument is of length 0.
- Fixed checkMAPCOUNTS() so it also works for maps that are
just
unamed
vectors (so in fact they are not maps) like the REJECTORF
pseudo-map
defined in the YEAST_DB schema.
- Version numped.
* : - fixed bug in "Lkeys<-" and "Rkeys<-" methods for
FlatBimap
objects
- centralized all Bimap methods in Bimap.R
- added the "keyname" generic to the Bimap interface
- got rid of 'Lkeys' and 'Rkeys' arguments in toTable's
signature
- added toTable method for FlatBimap objects
- some cleaning, reorganization and cosmetic improvements in
many
places
- version bump
* : - Renamed AnnDbMapDemo.Rnw -> AnnotationDbiDemo.Rnw
- Removed AnnDbMapAPIdemo-labmeeting20070123.txt
- Fixed bug in .dbUniqueMappedKeys.cached.symbol() that was
breaking AnnDbBimap
objects of (left or right) length 0.
- Small improvements to "show" methods for FlatBimap and
AnnDbBimap objects.
- Got rid of the 'keys' argument in "as.list" methods for
AnnDbBimap objects.
* : oops, forgot to adapt the vignette to the new signature of
"as.list" methods
for AnnDbBimap objects
* : some fixes in the man pages
* : some addition to the man pages
* : more work on the man pages
* : more work on the man pages (no more 'R CMD check' warnings)
* : temporarily disable checking of GO.db in examples given in
man
pages for checkMAPCOUNTS()
* : some doc improvements
* : cosmetic
* : cosmetic
* : removed go_obsolete.term_id column (useless and leads to
confusion) from the GO_DB schema
* : replaced some remaining occurences of "R environment" by "R
object" in the man pages of the ann db pkg templates
* : Dropped an superfluous reference to gopher6.
* : updated TODO.TXT
* : glups! I forgot to add man/Bimap.Rd
* : small update
* : small improvement
* : version bump
* : - Renamed "db" generic -> "dbconn" (for consistency with
the
recent addition
of "@ANNOBJPREFIX at _dbconn" in the ann db pkgs) and exported
it.
- Added "dbfile" generic (for consistency with the recent
addition of
of "@ANNOBJPREFIX at _dbfile" in the ann db pkgs) and exported
it.
- Added man page for "dbconn" and "dbfile".
- Removed @conn slot from AnnDbObj objects (not needed
anymore)
and exported
the AnnDbObj class.
- Version bump.
* : - Polished the AnnDbBimap class hierarchy: removed
AtomicAnnDbBimap (all
previous AtomicAnnDbBimap instances are now just AnnDbBimap
instances) and
renamed GONodeAnnDbBimap -> GOTermsAnnDbBimap (to align with
recent renaming
of the GONode class -> GOTerms).
- Added internal convenience generics and methods: "fromCol",
"toCol" and
"tagCol".
- Moved all the "as.list" methods from AnnDbBimap-envirAPI.R
to
Bimap.R (this
is temporary only, they will go in a .R file of their own).
- Added an "as.list" method for Bimap objects. Reworked
(mainly
simplified) all
"as.list" methods by using new "fromCol", "toCol" and
"tagCol"
convenience
methods. Fixed a bug in "as.list" method for AnnDbBimap
objects
(affecting
objects with at least 1 multi-valued right attribute).
- Reworked "as.character" method for AnnDbBimap objects.
- Version bump.
* : - Moved all the "as.list" methods from Bimap.R to new
BimapFormatting.R file.
- Also moved "from.colpos", "to.colpos", "fromCol", "toCol",
"tagCol",
"toLList", "toRList" and "toList" internal methods +
".formatList" and
".alignAnnList" internal functions + "as.character" method
for
AnnDbBimap
objects from Bimap.R to BimapFormatting.R
- Got rid of the 'direction' argument in "from.colpos" and
"to.colpos" generics.
- Removed "from.keys" and "to.keys" generics and methods.
- Renamed "foldListOfLists" internal function ->
".toListOfLists"
and moved
it to BimapFormatting.R
- Modified documentation consequently.
- Version bump.
* : updated TODO.TXT
* : bumped db roster from .99.4 to .99.5 in master index file
used
at the Gentleman Lab
* : - Turned "fromCol", "toCol", "tagCol", "from.colpos",
"to.colpos" generics
into normal functions and prefixed them with a "." (they are
not
used out
of the file they are defined in).
- Version bump.
* : - Fixed bug in "as.list" method for AgiAnnDbMap objects
(e.g.
as.list(agACCNUM)
was containing the NA and "multiple" values only).
- Fixed brace problem in MULTIHIT.Rd and ARACYC.Rd
- Version bump.
* : small addition to TODO.TXT
* : small addition to TODO.TXT
* : a few additions to TODO.TXT
* : more edits to TODO.TXT
* : improved comments for internal .formatList()
* : Fixed examples in all the ann db pkg templates ("as.list"
was
still used with extra keys arg, which has gone away
recently).
* : call callNextMethod() with no args in "revmap" method for
AnnDbBimap objects
* : small addition to TODO.TXT
* : - @ANNDBOBJ at _dbfile is now a function instead of a variable
- added "dbschema" and "dbInfo" generics with methods for
DBIConnection and
AnnDbObj objects (implementation is minimalist for now)
- added documentation (in particular, the _dbconn.Rd man page
in
the db pkg
templates was heavily reworked)
- version bump
* : checkMAPCOUNTS("GO.db") is back in the examples section of
AnnDbPkg-checker.Rd
* : Small bug fix in the db pkg templates. Version bump.
* : small edit
* : Fixed MAPCOUNTS.Rd in db pkg templates. Version bump.
* : renamed last remaining occurences of db_file -> dbfile
* : makeAnnDbPkg() now calls 'chmod 444' on the sqlite file so
it's
read-only
* : - added "dbmeta" generic and methods (no doc for now, will
come
soon)
- first real implementation of the "dbschema" and "dbInfo"
methods
- version bump
* : small addition to AnnDbObj-class.Rd
* : small fix
* : Improved dbschema(). Version bump.
annotationTools
* : corrected minor bug in ps2ps.R and bumped version number
aroma.light
* : Version: 1.5.2 [2007-08-10]
o Added encoding to some Rd files.
o Package pass R CMD check R v2.6.0.
arrayMagic
* : Bumped for LazyLoad.
arrayQualityMetrics
* : Debug the figure margins of heatmap and localisation plots
legends.
* : Replace the EBImage functions by graphics functions. No
dependencies of EBImage anymore.
* : fix heatmap and localisation legend problem
* : Added a TODO and fixed some wordings in the Figure captions
* : Corrected man pages
Add the function addXYfromGAL to handle arrays with multiple
blocks
* : - Creation of functions to avoid code duplication
- Use of lattice for the heatmap
* : - debug the main R code
- small modifications of the legends
- suppression of genes mapping and pm.mm per array (maybe to
reimplement
later with lattice)
- small corrections of man page
* : - Improvement of the Vignette
- Small correction of the code
* : - add the correct argument log.it in AffyRNAdeg
- remove sample names from boxplots when to many samples
- use of try() to call the plots to avoid partial reports
- precision added for Covariate in the Vignette
* : Better handling of NA
* : suppress warnings of dev.copy after qcStats plot production
beadarray
* : - added new options to createBeadSummaryData (see "method"
and
"trim" arguments) to allow mean, median, trimmed mean or
winsorized means to be calculated to summarise the values
from
each beat type on an array.
createBeadSummaryData.c code edited to allow new options
- "which" argument changed to "what" in getArrayData(). Also
added new arguments ("method" and "trim") for use by
createBeadSummaryData when what="residG", "residR" or "residM"
to
allow control over summarisation methods. Updated arguments
of
getArrayData() when called in other bead level plotting
functions.
- Added new arguments to boxplotBeads, imageplot,
plotBeadDensities, etc to accept these new arguments to
getArrayData (when whatToPlot="residG", "residR" or "residM")
- added FILL=TRUE to read.table() used in
readBeadSummaryData()
in response to message on BioC list from Ina Hoeschele about
error trying to read in BeadStudio version 3 data caused by
line
having incorrect number of entries
- updated help pages
* : - removed returnTIFF.c (not used anymore).
- NAs or Infs in imageplot() and createBeadSummaryData() now
excluded (previously set to zero).
- log2.na() (not exported) used in getArrayData() to avoid
throwing up a
warning message when 0's or negative values are log2.
- when useImages=FALSE in readIllumina(), x-, y-coordinates
read
from file are
now adjusted to start at 0,0 (useful for image plotting).
- readBeadSummaryData() has new argument ... to take
additional
arguments to read.table (quote="", fill=TRUE sometimes needed
for
BeadStudio
3 data). Reverses changes to readBeadSummaryData made in
1.5.10
and 1.5.7.
- new argument 'legend' in imageplot() to display range and
zlim
on plot.
- new argument 'arrays' in arrayNames() to get the name of a
selected array/s.
- new function getVariance() returns the variance for each
bead-type on each
array from an ExpressionSetIllumina object (calculated from
se.exprs and
NoBeads slots).
- SnpSetIllumina doesn't store se.exprs for each channel -
removed code
which assigns the se.exprs to a SnpSetIllumina object in
createBeadSummaryData()
- fixed broken link in BSData.Rd help page.
- default annoPkg argument in readIllumina() is
"illuminaProbeIDs" (not actually an annotation package, but
is
there to tell the user that ProbeIDs are used to identify
each
bead type (not Illumina IDs available in existing annotation
packages)
- createBeadSummaryData(): The phenoData slot is set to have
1
column 'sampleNames' which is set to the array names if no
phenoData information has been set. sampleNames are set to
either
the 'sampleNames' from phenoData, or the array names.
* : - phenoData in BLData object created by readIllumina()
contains
1 column 'arrayName' when no targets information is
specified.
- example BLData.rda object in package updated with phenoData
information.
* : - example BLData.rda object updated
* : - fixed bug in C code in calculateBackground
(readBeadImages.c)
function (was over-running end of array). Also made
backgroudSize
adaptive (was set to fixed size of 17x17 pixels in C code) and
is
more careful when at an edge (previously set background to 700
if
pixels went off the edge).
- fixed bug in findAllOutliers() (introduced in 1.5.11 when
&&
and || added to if statements. Inadvertantly added to which
at
the end of finaAllOutliers())
- fixed bug in SAMSummary() BeadChipSummary() - couldn't
handle
negative summary values and removed unknown 'v' variable
assigned
when missing_arrays argument was specified. Removed
missing_arrays argument, and added arguments 'samID',
'chipID'
and 'stripsPerChip' to allow user to choose which SAM/BeadChip
to
plot and specify the correct number of strips per chip.
Function
is more careful about plotting the data in the appropriate
row/column position, and returns a message it the user clicks
out
of range. Missing arrays are coloured white.
- removed unknown 'v' variable assigned when missing_arrays
argument was specified in plotOnSAM().
- getArrayData() now checks for out of range or NA 'array'
argument and returns a message
- createBeadSummaryData() checks for arraynm in all full list
of
array names in case 'array' has not been specified as
integer.
* : Added new versions of bead summary and bead level analysis
vignettes
beadarraySNP
* : Documentation
* : Improving import of Beadstudio data
* : bug fixed in R-code of Vignette
bgafun
* : Add new contributed package bgafun
Maintainter: Iain Wallace
bgx
* : sokal now shlib; sqrted mcse; changed rankByDE; read mumcse
into ExpressionSet; new z-statistic for ranking
* : Use sokal() rather than acf() (faster...) for rankByDE
* : Fixed allocation bug for returning output dir; reduced
default
burnin and iter
* : All ext C functions in bgx.so now. Registered sokal().
Minor
fix to problematic cex parameters in plotDEHistogram
* : Clean up screen presentation when reading in output
* : You can now combine output directories using readOutput.bgx
* : Include own version of boost header files
* : Check if removing -march=i386 solves liverpool linking
problem
* : Actually, check if -march=i486 works..
* : No need for README anymore, since we no longer depend on
external boost
Biobase
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
* : Add missing includes
* : should correct the DBL_MAX compilation error
* : no need for DBL_MAX
* : fixed a bit of the error messages
* : should correct the use of REAL macros in matchpt,
optimization
* : matchpt algorithm optimized for single argument calls, 10x
speed up
* : Time for a version bump so people using R devel >=
2007-08-06
will be able to install Biobase again (version 1.15.23
currently
online is broken for them).
* : bug fix in "corrected" matchpt, also matchpt(x, numeric(0)
now
returns NA indexes and Inf distances
* : man page correction for matchpt followin warning in check
* : my God, something happened to my logic: reverted most of
the
changes in matchpt for the last two days - they were buggy.
sorry
for that
* : I updated the man page of matchpt
* : matchpt to support integer for x and y
* : I removed the silly old cache_old.
matchpt now returns a data frame (index=integer,
distance=double)
with
row names.
* : updated man page
* : Just adding and removing this to verify that I got write
permission to the SVN.
* : Removed dummy.txt; verified I've got write permission to
SVN/Biobase.
* : Fixed copySubstitute() so it raises an error when it tries
to
substitute a symbol by an NA.
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : PUBLIC:
o Added anyMissing().
o Added support for missing values of rowMedians().
DETAILS:
o Now rowMedians() has an optimized C-level implementation.
There
is one implementation for real values and one for integers.
This
way an integer matrix does not have to be coerced to a double
(which would add 200% memory usage). Moreover, at the C-level
there is also an argument 'hasna'; if hasna=FALSE, missing
values
are not looked for resulting in a faster processing. At the R
level, this argument is currently hidden, but may be added if
found useful.
* : NChannelSet bug fix
- "_ALL_" should be required as a level in 'channel'
varMetadata;
it
was ommited during consturction (so channel info was labelled
'NA'
instead of '_ALL_' by default) and during channel selection.
- quietly add 'channel' to varMetadata
* : MIAME and phenoData bug fixes
- MIAME 'show' method uses 'notes' instead of 'other', as this
is
the
accessor
- (deprecated) phenoData had validity check in the wrong
place.
* : Add sublist_extract C function and subListExtract at R
level
subListExtract provides a fast way to extract a named element
from
a sublist of a list. Code that does something like:
sapply(L, function(x) x$foo)
can instead do
subListExtract(L, "foo", simplify=TRUE)
The unit tests are in subListExtract_test.R.
* : Improve error message for subListExtract edge case
(0-length
input)
When given list() as input, subListExtract will return
list(),
unless
simplify=TRUE, in which case an error is raised. The reasoning
is
that when the user asks to simplify, they expect a non-list to
be
returned. We can't determine what sort of vector they expect
so
an
error is raised.
* : Biobase::l2e now errors when given a list with NA in
names(L)
Prior to this patch, l2e would return an environment in which
an
element with name NA in the input was added to the
environment
with
key "NA". This situation now raises an error.
Error messages for bad arguments were also improved.
* : l2e now gives a warning if input list has duplicated names
* : Accomodate changes in base::package_version
- use numeric_version rather than package_version
- internal .as.numeric_version
- stronger checks on valid version comparisons
* : added commentary
* : esApply for ExpressionSet
* made esApply(X, MARGIN, FUN, ...) a generic
* method for exprSet same as previous functoin esApply
(inappropriately modifies FUN environment, breaking lexical
scope)
* method for ExpressionSet equivalent to
with(pData(X), apply(exprs(X), MARGIN, FUN, ...))
* Documentation to follow shortly
* : Further esApply revisions
- conform closely to original behavior
- update documentation
* : Correctly construct AnnotatedDataFrame with $<- and new
symbol
adf$sym <-,
added sym to data but did not add varMetadata["sym",].
Likewise
pData(adf) <- sym
would not add varMetadata for new cols in sym
* : (Silently) remove names from dimnames of assayData
Previously, named dimnames on assayData elements would produce
an
error when trying to 'harmonize' assay and feature/sample
names.
The
new behavior no longer produces an error, and silently
removes
names
from dimnames. Thanks to Benilton Carvalho for the original
report (in
affy) and Laurent Gautier for pointing toward ExpressionSet
* : fixed doc bug in openPDF -- it wrote of options(pdfViewer)
but
no cap V is desired
biocSurvey
* : tools to get overview of class usage etc for bioc software
review
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
biocViews
* : Fix bug in writeTopLevelView, unbound variable caught via
codetools
* : Fix inheritance for BiocView class
Don't double inherit Htmlized. Not sure why this was there in
the
first place and it was causing a method dispatch warning.
* : Update usage of sp.between to match latest changes in RBGL
* : Fix htmlDoc methods: include ... in signature
The method definition sig must have ... if the generic does.
* : The URL field is now a proper link in pkg "homepage" HTML
* : Remove unused htmlValue method
* : Add installation instructions (biocLite) to package
homepages
* : Update URL to point to release views
* : Output valid XHTML
* : biocViews is now a Biocore Team maintained package
* : Added terms for new annotation data pkg type.
These changes add new package names, a new ChipManufacturer
and a
Microarray type for CpG Island arrays.
* : Updates the version number for the new terms.
bioDist
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
biomaRt
* : Update of getBM with uniqueRows argument. getBM now returns
by
default only unique rows
* : Removed ensembl_transcript_id from getGene and getGO output
to
get gene-level annotation and reduce the redundancy in the
output. Converted 1:length code in for loops with seq.
* : Added uniqueRows argument to getLDS function. By default
getLDS
will return unique rows only
* : Defined methods on the Mart class to replace most @ symbols
in
the code
* : set show method for objects of class Mart
* : added setReplacementMethods to remove final @ symbols in
code
* : Removed braces that were not needed in Rd files
* : Moved XML from Depends to Imports in the package
DESCRIPTION
file and imported XML in the NAMESPACE
* : Put the require(RMySQL) call into a do.call statement to
avoid
warning message by R CMD check
* : Rewriting the vignette
* : Rewriting the vignette
* : Update of man pages
* : Fix in getBM when choosing list as output
BioMVCClass
* : removed all exprSet refs
Biostrings
* : - Small improvements to writeFASTA() implementation and
doc.
writeFASTA() is not a generic anymore: writing a BStringViews
object to
a FASTA file can now be done with write.BStringViews() (see
below).
- Added BStringViews-io.R file and started putting all
BStringViews IO related stuff.
Contains so far: FASTArecordsToBStringViews(),
BStringViewsToFASTArecords(),
read.BStringViews() and write.BStringViews().
Deprecated "BStringViews" method for "file" object in favor
of
function
read.BStringViews().
- Renamed arg 'sep' -> 'collapse'.
* : Check OK. Version bump.
* : - Added the "desc<-" generic with a replace method for
BStringViews objects.
- Got rid of a few more TODOs in the doc.
* : Fixed bugs in "nchar" method for BStringViews objects.
Revisited semantic and implementation of the "==" methods for
BString and BStringViews objects. Got rid of more TODOs in
the
man pages.
* : small fixes in the doc to make R CMD check happier
* : small fix in the vignettes
* : Completed doc for constructor-like functions views(),
adjacentViews() and BStringViews().
* : Added man page skeleton for Longest Common
Prefix/Suffix/Substring family of functions (work in
progress).
* : Added man page skeleton for the new BStringPartialMatches
class
(work in progress).
* : Check OK. Version bump.
* : added a few comments in naive_fuzzy_search() C code
* : fixed small bug in "nchar" and "width" methods for
BStringViews
objects
BufferedMatrix
* : Fix MoveStorageDirectory() for windows build
* : add rowMedians() (should only be used in RowMode)
buildBioC
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
CALIB
* : fix warning because of function "[ <-".
fix bug of missing value in spike intensity and gene
intensity.
fix bug of empty clone id name when normalizing data.
* : bumping version
Category
* : Add first draft of cb_test
cb_test is a flexible hypothesis testing tools for
discovering
interestings chromosome bands relative to a selected gene
list.
The
tools supports local and global tests which can be carried out
in
a
top down or bottom up fashion on the tree of chromosome
bands.
* : Deprecate isConditional generic
Replace use of isConditional() with conditional(). This
resolves
strange warning messages and check failure due to an improper
reassignment of the conditional generic.
* : Support for org.XX.eg.db annotation packages
* : Create a helper function to make hyperGTest methods more
flexible
* : Modifications to methods for KEGG and PFAM data to include
hyperlinks to KEGG and PFAM (Sanger institute) websites in
output
from htmlReport().
* : Add digits and summary.args arguments to htmlReport
This allows user to specify the number of display digits for
numerical
fields. htmlReport no longer accepts '...' and uses
summary.args
instead to pass additional arguments to the summary method.
* : Moved htmlReport and summary methods for KEGG and PFAM data
from GOstats to Category. Also changed the signatures for the
htmlReport to coincide with the refactored htmlReport method.
* : Update examples to use hgu95av2.db
* : Move GO and KEGG from Depends to Suggests
Actually, we now suggest the *.db versions. The code should
work
if either is available. A downside of this approach is that
the
dependence is implicit (we don't call require). So I've added
a
comment with require("GO"), etc to help remind us.
* : Fixup some man pages to remove warnings during R CMD check.
No
version bump.
* : Added species abbreviation to html links for htmlReport of
KEGG
data. Currently only hsa, mmu and rnu are used with hsa as
default.
* : GO2AllProbes,DatPkg-method now only queries for GO IDs that
exist
In making Category/GOstats compatible with db-based ann pkgs,
we
encountered some problems with AnnotationDbi raising an error
when
asking for a key that doesn't exist. We plan to fix the
env-API
to Do
What Environments Do, but in this case it was easy to have
the
code
simply not ask for things that won't be there.
* : Fix references in Category vignette
Thanks to Francois Pepin for the report.
* : Add a TODO list for Category
* : Add getGoToEntrezMap_db, big speed up for hyperGTest "over"
This patch adds DB-specific code (with custom SQL,
unfortunately)
that
speeds up the categoryToEntrezBuilder step of hyperGTest for
GOHyperGParams when doing a test for over representation. The
under
representation case is special in that we need to keep the GO
IDs
that
don't have any of the selected Entrez IDs annotated at them
and
so
that is left as a TODO. We also need to add DB-specific code
for
the other gene set collections (KEGG, PFAM, etc). Also, the
method of
dispatching on DB-based or not ann pkgs is not ideal.
* : Add some comments to getGoToEntrezMap_db
* : Add support for under-representation for
getGoToEntrezMap_db
* : Use subListExtract in getUniverseViaGo
* : Add Org.XX.egDatPkg to class exports
This class is used only internally for providing a common
interface to
annotation data coming from the new org.*.eg.db packages. But
it
should be exported so that others can make extensions of the
Category-based code.
* : Add more doc for cb_test
* : Add some doc for *_test_factory internal funcs and fix args
* : Rename tree_iter => tree_visitor
* : Rename topdown_iter and bottomup_iter
They are now called topdown_tree_visitor and
bottomup_tree_visitor
* : Add doc for internal func tree_visitor
* : add mouse chromosome band parsing for HyperG
* : Rename chrBandInciMat => MAPAmat
chrBandInciMat is still available, but deprecated. The
behavior
of
MAPAmat has changed (see man page). Any users of MAPAmat will
need to
revisit their code.
* : Remove base_cbind workaround since Matrix no longer
clobbers
base::cbind
* : Rename Category::gseaperm => gseattperm
This function is hard-wired to use rowttests. Eventually,
more
flexible version should be written, but for now we will rename
to
make
clear what this function does (and doesn't do).
* : add helper function for the clean procedure of the
chromosome
band definition
add helper function to get organism name
rename parsing functions using Hs and Mm instead of hsa and
mmus
simplify Mm parsing function
* : Cleanup MAPcode.R changes
- Fix deprecation of cb_parse_band_hsa.
- Remove debug print statement
- Call func directly instead of using do.call
- Add checkChrOrg to consolidate checking of organism
* : Fix helper function isDBDatPkg so it will work with non
Affy
chip packages
Now we check for the name ending in '.db' rather than relying
on
getAnnMap (which searches for DB if available first). Not
sure
this
is best.
* : Fix annotation<- method so that it updates the datPkg slot
* : Add error message for org.Sc.sgd.db not supported
Hopefully this is temporary.
* : Fix annotation<- method, value must be character, not ANY
This patch also resolves the Rd warning.
* : Add a show method for ChrBandTree objects
* : Add treeLevels and level2nodes generics/methods for
ChrBandTree
objects
* : Use toSQLStringSet instead of sQuote to build SQL
statements
sQuote should NEVER be used for building SQL or anything
other
than
display messages. In non-C locales, sQuote now provides fancy
quotes
which are therefore useless for single quoting strings. We
now
use
the newly added toSQLStringSet from AnnotationDbi to created
SQL
value
lists. This should resolve the error seen in GOstats on
Windows.
* : Some enhancements to cb_test
Allow different p-value cutoffs to be specified for next
level
testing
and for determining significant nodes for a conditional test.
* : Change maintainer from Seth to Robert
Category, GOstats, graph, graphPart, hypergraph
* : fixed up Category to deal with db_conn changes
* : one more try
* : fixed a typo
cellHTS
* : typo correction
* : correction
* : typo correction
* : typo correction of Rd files
* : Adding an extra check for the controls
* : Correction of 'writeReport' related with the case when
there
are no positive controls in the screen.
* : Improvement of the function that does the tooltips. It's
now
much quicker!
* : Add a import function for plate files obtained from
EnVision
Plate Reader
* : typo correction
* : Specifying the error messages in "readPlateData".
Just to be sure: added a consistency check test for well
format
of column "Well" of the gene annotation file.
* : typo corrections
* : typo correction
* : Typo correction
* : Updates of the main vignette due to updates in packages
biomaRt
and Category.
* : correction
cellHTS2
* : Starting the package.
* : More updates
* : more updates
* : more updates
* : correction
* : correction
* : More updates
* : completing the package
* : improvements
* : more updates
* : Cleaning up
* : Adding the modified files (cellHTS class now extends
NChannelSet class)
* : An attempt to (slightly) clean up to links to S4 classes
from
Biobase in the man pages.
* : Add ROC class, import function and example set for
HTanalyser
input files
* : correction of links in man pages
* : Add getTopTable function
* : Adding function getMeasureRepAgreement
* : Add function to determine Z'-factor and dynamic range
* : Adding writeReport and imageScreen function
* : add function to plot plate effects
* : Typo corrections, added biomart query data set
* : Add example of batch usage
* : Adding vignettes and man page for biomart data set
* : Typo correction
* : typo correction
* : Adding functio to make a screen plot with the plate
configuration.
* : Correction
* : Adding a function called convertOldCellHTS that converts an
old
S3 class cellHTS object to S4 class cellHTS object(s)
suitable
for the cellHTS2 package.
* : typo corrections
CGHcall
* : added the CGHcall package
Maintainer: Sjoerd Vosse
cghMCR
* : Man page updated.
clusterStab
* : Bumped for LazyLoad.
codelink
* : 1.5.16
- FIXED weird return in codCorrect().
- ADDED experimental C code in src/ to fast reading of
Codelink
files. The
function readCodelinkFiles() works pretty much the same as
readCodelink() but
is much faster. Currectly it reads data as a Codelink object.
In
addition, it
reads also the feature_id field, that can be used for
creating
suitable
CodelinkSet objects.
- ADDED this comments for the first time to the svn log.
- ADDED summary method for Codelink objects. Actually it
outputs
a summary of
the flags.
convert
* : Add converters to NChannelSet
- RGList, marrayRaw
- bug fix to marrayNorm -> ExpressionSet
- Also updated documentation to indicate that -> exprSet
converters
are to deprecated classes
* : Tweaked RGList convert
- previously misunderstood 'targets' to contain a list of
file
names,
but is actually a data frame.
* : split the R source of the package into several files, so
they
can be
more easily copied to other places
DEDS
* : removeUnknownFunction
DNAcopy
* : Fixed help files to address warning messages.
* : Fixed the unused variable warnings from gfortran
* : This is version 1.11.2 with p-value code for the
change-points
(3 new files).
* : p-value code files didn't go through. Now they should.
* : removed ostat print statement & used k=2
DynDoc
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : Bumped for LazyLoad.
EBarrays
* : major update of EBarrays, initial checkin of version 2.0
EBImage
* : ImageMagick requirement version bump. configure to follow
* : new, fully rewritten vignette
* : no info
* : minor typo fixes in man
* : version check of ImageMagick in configure script
* : awk is strange, split($1, x, ".") did not work, for
$1="6.2.4",
neither did split($1,x,"\."). workaround
* : added drawtext. still devel, but working :)
* : Added possibility to draw text annotations on images:
drawtext,
drawfont functions
* : bug in zernike, corrected (was: no summation over x,y)
* : more accurate drawtext initialization and !NULL checks for
font
and text labels in the c-module for drawtext. trying to
resolve
man pages error on Mac BioC build
* : forgot the new Windows DLL, added
* : drawtext example exexcution prevented on Mac to pass check
until the problem with this particular build can be tested
(no
hardware available). The problem is most likely to be in font
allocation.
* : minor configure output modifications
* : I edited the Image() function and fixed its man page
* : reverted aliases in man::constructors.Rd that mess up
index;
corrected Sys.getenv("R_PLATFORM") in drawables.Rd to
determine
MacOS
* : fully refurbished man pages
* : man page for package contents
* : version bump because of deprecated dot-functions
* : corrected one forgotten deprecated function
* : I added a display method for matrices, currently it just
converts into a
greyscale image
* : added: animate,array-method, following the code by Wolfgang
for
display,array-method. Added usage clause in the help entry
* : added display options
* : colorize argument for display if used with IndexedImage
* : updated examples in man pages, checked up FIXME things
ecolitk
* : - added a label to chunk 16 (there seems to be a bug
with affy)
- bumped version number
edd
* : Bumped for LazyLoad.
exonmap
* : Changes in splicing.index() : added a parameter for use of
median/mean in gene level expression and fixed the method of
exon
selection for gene-level estimate.
* : fixed plotting bug in plot.gene
* : fixed hardoded config directory to look for environment
variable specifying the path
* : fixings in splicing anova
explorase
* : * Add quick search bar and column visibility panel.
* Add Canberra distance, meant for metabolomics data (ie
non-detects)
* Support hierarchical clustering with all distance measures
(angle, cor,
euclidean, and canberra) instead of just euclidean.
* Pattern finding cleaned up. GUI supports changing the
"unchanged"
fraction and updating the results. Pattern finder no longer
creates a
new result column each time it is run on the same set of
conditions.
Selecting a large number of conditions activates the
scrollbars -
GUI no
longer reaches off-screen.
* Limma frontend works with user-selected subsets of
conditions.
* Long titles in column headers handled better with ellipsis
and
tooltips.
* More robust file loading with warning dialogs if problems
detected.
* Misc other bugs fixed.
* Initial support for network data and visualization -
disabled
for
release.
externalVector
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
fbat
* : replaced 'SaveImage: Yes' with 'LazyLoad: true'
* : deleted an unmatched right brace in 'getFounders.Rd'
* : fixed a few warnings about 'uninitialized' variables:
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include
-I/home/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include
-fpic -g -O2 -Wall -c FBAT.c -o FBAT.o
FBAT.c: In function 'countLines':
FBAT.c:2142: warning: 'tmpnc2' may be used uninitialized in
this
function
FBAT.c: In function 'oneNuclearFamily':
FBAT.c:1859: warning: 'sex2' may be used uninitialized in
this
function
FBAT.c:1859: warning: 'sex1' may be used uninitialized in
this
function
FBAT.c: In function 'decomposePed':
FBAT.c:1986: warning: 'i' may be used uninitialized in this
function
FBAT.c: In function 'checkoneNuclearFamily':
FBAT.c:1667: warning: 'sex2' may be used uninitialized in
this
function
FBAT.c:1667: warning: 'sex1' may be used uninitialized in
this
function
FBAT.c: In function 'checkdecomposePed':
FBAT.c:1590: warning: 'i' may be used uninitialized in this
function
FBAT.c: In function 'checkCompatible':
FBAT.c:1404: warning: 'start2' may be used uninitialized in
this
function
FBAT.c: In function 'fbat':
FBAT.c:43: warning: 'start2' may be used uninitialized in
this
function
* : fixed the problem of 'no visible bindings'. Thanks Dr.
Lazarus
for the help!
* : Replaced the tab with 7 whitespace to avoid the warnings:
arning: Nonconforming tab character in column 1 of line 1
Warning: Nonconforming tab character in column 1 of line 4
Warning: Nonconforming tab character in column 1 of line 5
Warning: Nonconforming tab character in column 1 of line 6
Warning: Nonconforming tab character in column 1 of line 9
Warning: Nonconforming tab character in column 1 of line 13
Warning: Nonconforming tab character in column 1 of line 48
Warning: Nonconforming tab character in column 1 of line 49
* : Bumped for Lazyload.
flowCore
* : Adding unit tests from Josef and Ryan.
* : added some code to allow for varLabels accessing and
setting
* : modify the namespace to export the methods
* : remove parenId from class definition of gates
* : Many changes. Mostly related to filterSets, but there is a
bunch of other stuff as well. See the flowcyt-devel mailing
list
archives for info
* : Adding extra files
* : fixed summary problems
* : fix documentation
* : Improvements to the filterSet filter() code and summary()
code
flowSet(...,phenoData) convencience function to wrap
as(,"flowSet") and phenoData<-() into a single
operation if desired.
split() now takes an optional flowSet=TRUE argument to get a
flowSet instead of a list. Allows split
operations to optionally be "smart" (e.g. manyFilterResult
and
filterSet put an indicator of WHICH filter
generated the flowFrame)
manyFilterResult implementation improvements
manyFilterResult documentation improvements
* : Fix read.FCS for case when non-UTF8 encoding (e.g. FlowJo)
is
used in an FCS file
flowQ
* : fixed some minor documentation issues
flowUtils
* : reimplementation and refactoring of gating-ML
* : Adding extra files
* : fixed missing html links
flowViz
* : separated out panel function for xyplot.flowset, and
removed
rgl as a dependency
* : fixed problem in last commit
* : changes in filter boundary for rectangleGate
* : attempt at filter boundary method for combined filters
* : more fixes for separated panel function
* : added missing parentheses
* : fixed some small documentation issues
* : displayFilter included in panel function, updated docs
* : commented out parallelCoordinates.rgl
* : documented prepanel and panel functions, updated version
* : documentation updates
genefilter
* : Fix nsFilter bug when var.filter=FALSE
Thanks to Swann for the bug report during BioC2007.
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : Use subListExtract instead of sapply to improve filtering
speed
* : genefilter now depends on recent Biobase
* : Fix use of subListExtract, need simplify=TRUE
GeneMeta
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
geneplotter
* : added na.rm=TRUE in range() for axis limit computation
* : Added multiecdf and multidensity methods for matrix
(they are quite trivial, they call formula with x~col(x))
* : I fixed a bug that occur when argument was list of length 1
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : better treatment of xlim in multidensity
* : fixed man pages and default argument values
* : col parameter now gets passed to points in order to control
the
point colors
* : Defaults of xaxs and yaxs now match those of plot.default
* : Fixed typo: seq(alog=...) --> seq(along=)
* : Update examples to use sample.ExpressionSet
Several examples used sample.exprSet (deprecated exprSet);
sample.ExpressionSet is not a 1:1 replacement for
sample.exprSet,
so
example results are different (generally, two groups rather
than
three).
* : Makesense now uses getAnnMap
* : Deprecate Makesense 'eSet' method
'eSet' method does not make sense for the virtual class (no
guarantee
of exprs method), but derived classes with defined exprs
could
have
relied on for this method so cannot be removed immediately.
Added method for ExpressionSet.
* : Deprecate identifyLines
Not currently exported from the name space, not used
internally
* : Clarify documentation to indicate ExprssionSet, rather than
eSet
* : geneplotter now imports AnnotationDbi
This is needed so that internal calls to mget dispatch
properly
when
the object is a db map from AnnotationDbi rather than an
environment.
* : simple changes to pass check on 2.6
* : bump version for vignette visualize.Rnw fix
* : make plotExpressionGraph example work
GeneR
* : Supression of &.segSet and |.segSet shortcut
* : changes
GeneSpring
* : Bumped for LazyLoad.
GeneticsBase
* : replaced 'SaveImage: Yes' by 'LazyLoad: true' to fix the
following warning message:
WARNING: true value of 'SaveImage' is deprecated in favour of
'LazyLoad: true'
* : deleted an unmatched right brace on line 7 in
'makeMarkerInfo.Rd'
* : replaced 'print.xtable' with 'print' since there is no
'print.xtable' in the library 'xtable'.
* : (1) replaced 'fun.lo' and 'fun.hi' in 'binsearch.R' with
'val.lo' and 'val.hi', respectively, since no visible binding
for
global variables 'fun.lo' and 'fun.hi'.
(2) replaced 'fname' with 'gformat' in 'readGenes.R' since no
visible binding for global variable 'fname'
(3) replaced 'maker' with 'nMarker' in
'makeCCodesAndTables.R'
since no visible binding for global variable 'maker'
* : replaced the unknown encoding 'Â*A' with 'mu' in 'xbat.Rd'.
Also
added a few '$' to distinguish
math symbol and text.
* : added 'haplo.stats' to 'Depends' section in 'DESCRIPTION'
* : fixed a bug: readGenes.ped.cpp:86: warning: 'tmpnc2' may be
used uninitialized in this function
* : removed the comment: #importFrom(combinat, rmultz2)
* : deleted 'combinat' from 'Imports' field
* : Deleted 'haplo.stats' from 'Imports' section to avoid
compiling
error
* : We added the missed argument 'founderOnly' to fix a bug
pointed
out by Dr. Kouros Owzar. Thanks Dr. Kouros Owzar!
* : added a check if founder only data is required at the
beginning
of the the function 'desMarker'
* : replaced the function 'geneSet2Ped2' by 'geneSet2Ped' so
that
more meaningful error info will be output when error occurs.
GeneticsDesign
* : Fix documentation for power.case.ctl: swap description of
kp
and alpha
* : Integrate changes to power.casectrl from Michael Man.
* : Rename files 'power.casectl.{R,Rd}' and
'plot.power.casectl.R'
to match the function names. 'casectl' --> 'casectrl'
* : Remove binsearch() and use (bug-fixed) gtools::binsearch()
instead
* : Expose power.genotype.conti() function for estimating power
for
genetice studies using baseline measurements via simulation.
* : move pw() out of plot.power.casectl.R into a separate file.
Note that it needs to be documented before exporting.
GeneticsPed
* : cleanup
* : fixed a warning: sargolzaei.c:72: warning: 'N' is used
uninitialized in this function
* : generic strings
* : move
* : removing package GeneticsPed from depends
* : cleanup
* : subject --> individual
* : prune function
* : accesor functions
* : move
* : move
* : datasets
* : no need for t(); added utilities hwp() and gpLong2Wide
* : added utilities hwp() and gpLong2Wide
* : some formatting and note on utilities hwp() and gpLong2Wide
* : suggests genetics and note on use
* : fixes; I still have to learn how to use this function
* : now in datasets.Rd
* : we need better implementation
* : removal of codeUnit; genetics is in depends now
* : we have genetics in depends now
* : subject --> ind
* : better integration
* : note
* : use of slot accessors
* : commenting some funcs for the moment
GeneTraffic
* : Bumped for LazyLoad.
GEOquery
* : Fixed sort problems in GDS2eSet and GDS2MA
* : turned on the Windows build again
* : 2.1.9
=====
* removed R.utils dependency to fix windows build issue
* added gunzip() function (from R.utils), necessary because I
need to reset
the connection while reading
* : 2.1.10
======
* Windows parsing of GSEMatrix broken, so disabled it until
it
can be fixed.
* : 2.1.11
======
Fixed vignette to deal with lack of GSEMatrix parsing on
windows.
GGtools
* : for the ggexplorer.org site
* : found bug need to fix on plot_mlp
* : ok
* : site support resources
* : many changes to deal with reflectance of fitting function
and
erroneous plotting of gene locations in trans analyses
plot_mlp
* : full image of site
* : fix global in snps3Pto.
* : some man fixes
GlobalAncova
* : avoid strange error in examples
* : correction in globaltest function call
* : added C-implementation of permutation test
* : deleted needless comments
* : corrected .bib file
globaltest
* : - removed several tiny bugs
* : Added quotes to geneplot and sampleplot legends
* : Synchronized the definition of combine with Biobase
* : Corrected documentation of "combine"
GOstats
* : Deprecate isConditional generic
Replace use of isConditional() with conditional(). This
resolves
strange warning messages and check failure due to an improper
reassignment of the conditional generic.
* : Specify required ver of Category
* : Modifications to methods for KEGG and PFAM data to include
hyperlinks to KEGG and PFAM (Sanger institute) websites in
output
from htmlReport().
* : Add digits and summary.args arguments to htmlReport
This allows user to specify the number of display digits for
numerical
fields. htmlReport no longer accepts '...' and uses
summary.args
instead to pass additional arguments to the summary method.
* : Moved htmlReport and summary methods for KEGG and PFAM data
from GOstats to Category. Also changed the signatures for the
htmlReport to coincide with the refactored htmlReport method.
* : Unify access to annotation maps
* : Refactor makeGOGraph, simLL for GO.db compatibility
Compatibility with GO.db requires a change in signature for
these
functions because there is no longer a map to Entrez Gene IDs
within
the GO.db package. These functions now take a eg2go.map which
is
expected to be an object with an environment-like interface.
* : Fixes for GO.db compatibility for shortestPath and
makeGOGraph
example
shortestPath has new argument where the mapping from GO to EG
must be
specified.
* : GOstats vignette now using hgu95av2.db
* : Attempt to fix GOvis vignette for compatibility with
db-based
pkgs
* : Backward compat fix for makeGOGraph, simLL for DB-based ann
pkg
use
We introduce new arguments at the end of the signature,
mapfun
and
chip, which allow for DB-based ann pkg compatibility without
breaking
existing code.
* : Move .get_eg_to_go_fun to zzz.R and add 'reverse' argument
The reverse argument can be used to obtain a go_to_eg map and
is
used by shortestPath.
* : Backward compat fix for shortestPath and DB-compat
* : Use subListExtract in makeGOGraph
* : GOstats::GOLeaves is deprecated in favor of graph::leaves
An example of using leaves was added to GOviz.Rnw.
* : Change maintainer from Seth to Robert
Category, GOstats, graph, graphPart, hypergraph
* : fixed a typo
goTools
* : Bumped for LazyLoad.
gpls
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
graph
* : Improve error message when trying to remove nodes not
present
in a graph
* : Add a graphData slot to class graph
graphData is intended to hold graph-level attributes. This
patch
also
adds definitions for graphData generics, but no methods.
* : I improved the handling of the incoming matrix in the matrix
->
graphAM
coercion method.
There are a number of warning messages from R CMD check
regarding
new
classes and methods that fall in someone else's reach.
* : Refactor multiGraph, do not extend graph
Since graph has an edgeData slot, multiGraph should not
extend
it.
This patch adds an edgeData slot to edgeSet and a nodeData
slot
to
multiGraph.
Also updated and added notes to the GraphClass document
* : More notes on multiGraph
* : Improve degree method and add unit tests
* : Add more unit tests for inEdges
These tests exercise common calling patterns where Nodes arg
is
missing.
* : Add a leaves method to compute the leaves of a graph
A leaf of an undirected graph is a node with degree 1. For
directed
graphs, leaves are computed with respect to in or out edges;
leaves
are the nodes with no in edges or no out edges.
This patch adds a leaves generic and a method for graph
objects.
* : Fix graphAM inEdges method defs: args were in wrong order
This fixes a unit test failure seen in inEdges for graphAM
objects.
The function def signature had the arguments in the wrong
order.
* : remove commented code
* : Add alternative GXL even parser: graph_handler
This XML event parser handles GXL files using environments
for
intermediate storage and only creating a graph instance after
parsing
is complete. This reduces copying and dramatically improves
runtime
performance.
* : Use getExportedValue instead of require where possible for
XML
package
For functions that provide optional features based on the XML
package,
we now use getExportedValue instead of require("XML") to
avoid
attaching the XML package to the search path and polluting
the
user's
visible namespace. An exception is the toGXL function which
returns
an XML object. This function still calls require.
* : Change maintainer from Seth to Robert
Category, GOstats, graph, graphPart, hypergraph
* : serialized MAPK signaling pathway graph
* : trying to put some documentation in place
* : added man pages for the multigraph classes
graphPart
* : Change maintainer from Seth to Robert
Category, GOstats, graph, graphPart, hypergraph
GSEABase
* : incidence(<GeneSet>, ...) and (<GeneSetCollection>)
- also minor bug fixes
* : incidence reuse + minor speed refactor
* : Allow for missing attributes in Broad xml files
* : Preliminary KEGGCollection
* : GeneSetCollection constructor revision
- use idType, setType as well as 'object' in dispatch
- idType, setType _after_ ..., so unamed args are not
automatically
matched (e.g.., because we are constructing a gene set
collection
from several different gene sets, and don't want/need to
specify
idType, setType
- Multiple dispatch and allowing for 'missing' arguments
probably
makes callNextMethod dispatch too complicated to work out
reliably.
* : Bug fixes on GeneSetCollection
* : GeneSetCollection from old or new annotation files
- User-transparent AnnotationEnvIdentifier,
AnnotationDbiIdentifier
* : More GeneSetCollection constructors
* idType=AnnotationIdentifier(), setType=GOCollection()
* object=ExprssionSet, setType=KEGGCollection() |
GOCollection(),
to
construct sets just with AnnotationIdentifier's found in the
ExprssionSet
- Use evidenceCode in GOCollection to restrict to particular
evidence
Reverted to a single AnnotationIdentifier class
* : Minimally improved show method for GeneSetCollection
* : Bug in show
* : GeneSetCollection logic
- &, |, setdiff for character, GeneSet
Accessors for GeneSetCollection
- geneIds, geneIds<-
* : mapIdentifiers for GeneSetCollection, plus bug fix for
geneIds<-
* : Documentation updates
* : getBroadSets bug fix, and retrieve character vector of
Broad
gene
card names
* : Add keggIds to KEGGCollectoin, [[,GeneSetCollection,GeneSet
Also:
- setters for GOCollection members
- slightly better warnings when maps are not 1:1
* : Add IdFactory, AnnotationIdFactory
- Not exported
- Construct identifier classes, perhaps derived from
AnnotationIdentifier
Bug fix to verbose mapIdentifiers
* : Untangle a bit of S4 inheritance
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : Identifier and Collection extensions
- Make it easier to add new GeneIdentifierType and
CollectionType
classes
- add identifiers and collections for common annotation-based
maps
* : Additional GeneSetCollection constructors
- from any CollectionType or derived class
- Also Pfam and Prosite are better as collections than
identifiers.
* : URL of getGeneSets set correctly on windows
Windows 'file' urls should be file:///c:/..., but were left
unmodified
* : Attempt to coerce GeneSet identifiers when subsetting
ExpressionSet
Mapp from GeneSet identifiers to appropriate
AnnotationIdentifiers for
the ExpressionSet, if necessary and possible.
* : Unit test for ExpressionSet subset
* : Additional example data file (single Broad gene set)
* : More concise 'show' and 'details' for GeneSet, GeneColorSet
- 'show' provides summary information
- new generic 'details' and methods call 'show' but display
less-frequently needed details (e.g., setIdentifier)
- GeneColorSet method places phenotype data before details.
* : GeneSet constructor from BroadCollection
- urls argument provides source (including file) for GeneSet
- uses getBroadSets internally
* : Revert premature use of new naming scheme
geneIds will remain as such, rather than ids
* : Revised vignette
* : importFrom rather than depend on XML
- avoid unnecessary clutter in user name space
* : Documentation updates
* : Minor documentation and unit test changes
* : Minor documentation and unit test changes
* : Version bump to be included in 2.1 release
* : Remove stray line from NAMESPACE
* : Make setIdentifier behave more as advertized
- Most changes to a gene set cause the setIdentifier to be
re-calculated
* : Minor code beautification
* : Vignette updates
* : Vignette and package description tidy
* : add number of unique identifiers to 'show' method
Harshlight
* : Corrected author's name
Eliminated warning in sim.Rd
Updated c code: boundary correction
Update R code: substitution bug
* : Updated version number
hypergraph
* : Change maintainer from Seth to Robert
Category, GOstats, graph, graphPart, hypergraph
Icens
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
idiogram
* : Changed the DESCRIPTION to reflect the real author...
* : Re-made some old pre-2.40 objects...
* : Fixed a small bug that messed up the colors when plotting
point
style plots
iSNetwork
* : updateing to ExpressionSet
* : more updates - exprSet being replaced by ExpressionSet
* : last of the exprSet-ExpressionSet changes
* : added a missing KEGG dependency
* : fixing a failed variable reference
iSPlot
* : Bumped for LazyLoad.
keggorth
* : fixed links
* : indRender added
* : ok
KEGGSOAP
* : removed all calls to require etc in man pages - these should
be
handled
by package dependencies
lapmix
* : added version specification to the dependency on R, since R
CMD
check wants that
limma
* : 17 Aug 2007: limma 2.11.10
- topTable() and toptable() have new arguments p.value and
lfc,
allowing
users to cut the gene list on adjusted p.value and fold
change,
rather
than just taking a set number of genes as before.
* : 31 Aug 2007: limma 2.11.11
- correction to loessFit() because lowess() function now in
stats
instead of base.
- other documentation fixes to pass package check in R 2.6.0
- Ritchie et al (2007) reference added to User's Guide and to
the
backgroundCorrect and normexp help pages.
* : 8 Sep 2007: limma 2.11.12
- edits to loessfit.Rd to better acknowledge lowess and loess
authors.
* : limma 2.11.13. Bug fix to as.matrix.vsn.
* : 25 Sep 2007: limma 2.11.14
- plot character and size can now be passed to volcanoplot()
as
arguments
- add backgroundCorrect(method="normexp") to automatic test
suite
(not user visible)
logicFS
* : Added NAMESPACE
* : Fixed a bug in vim.norm.
lumi
* : I removed the version number from 'vsn' in the 'Suggests'
field
it appears that R CMD build did not deal gracefully with it.
* : 1. Add a background adjustment function
2. detectionCall function can return AP matrix
* : Include inverse VST function for lumiBatch objects after
lumiT
or lumiN processing
* : From version 1.3.18-1.3.26
1. Updated the vst function in version 1.3.25. (estimate the
c3
based on the background probes).
2. Updated the inverseVST and other related functions to
allow
the recover to the raw scale of the preprocessed data.
3. Added the evaluation of VST vignette
4. Updated the lumi vignette
maDB
* : unsupported on Windows
made4
* : fix to overview, factor(classvec)
* : new version of heatplot, includes a scale bar
* : Added new function pretty.dend. This draws a dendrogram, a
color bars for sample co-variates under the dendrogram. Added
new
functionality to overview and to heatplot. Heatplot now uses
heatmap.2 and includes a scale bar. Also bug fixes to
overview
and heaplot
* : Added new function pretty.dend. This draws a dendrogram, a
color bars for sample co-variates under the dendrogram.
* : Update and new functions on plotting functions, plotarrays,
plotgenes, plot.bga, plot.ord, plot.suppl
maigesPack
* : Initial check-in
Maintainer: Gustavo H. Esteves
makePlatformDesign
* : fixing duplicated functions
MANOR
* : changement dans le code C de nem pour suppression d'un
Warning
sur Windows Server
* : suppression des warnings pour 'global binding'
* : section \usage: methodes S3 correctement decrites
* : initialisation de la variable tmpV dans Rnem_exe.c
* : 1.9.6: suppression de qq warnings
maSigPro
* : ascii fixes
matchprobes
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
MergeMaid
* : Sep 23th updates by SZ
MLInterfaces
* : primitive sketch of schema approach
* : ok
* : clean up file structure to Bmethods for things to be
deprecated
eventually
* : Bmethods.R absorbs all the *Interfaces.R, they will
eventually
be deprecated
getting ready to introduce the schema method
* : schema support in
* : small vignette on schema based approach
* : separating legacy methods/constructors, moving out INIT.R
* : includes some xval support in MLearn
* : includes improved varImpStruct, README
* : README text edits
* : improved xval
* : drop nxval
* : drop MLearn.wx
* : minor update
* : minor fixes
* : passes check, new xval paradigm
* : added doc on balKfold
* : balKfold doc
* : feature selection now in place
* : much of the cross-validation infrastructure (partition
balKfold, fsFun) tested
* : includes history of feature selection
* : more info in README.txt
* : fix terms call
* : fsHistory doc
* : readme
* : rda infrastructure beginning
* : various rda support added
* : passing check
* : MLint_devel vignette improved
* : commented deprecation calles in, added slda support
* : doc fixes, pairing down namespace
* : ada dependency added
* : added Kfold
* : why not in commit?
* : getting the MLprac2_0.Rnw vignette in
* : practicum upgraded to MLearn/learnerSchema/xvalSpec
paradigm
* : Kfold forgotten
* : forgot vignette index entr
* : fixed flaw in new vignette
* : needed Suggests keggorth
MVCClass
* : removed all exprSet refs
* : updated and bumped version no
oligo
* : Fixing dependencies
* : Adding a missing file
* : Using normalize.quantiles.use.target for more efficient
normalization
* : initialize for DBPDInfo has .Object, ... now, allowing
xba240
to install ... more edits may be needed
for other initializers
* : bump version for initializer fix
* : Fix crash in affyio due to extra call to fclose
Also updating required version for oligo
* : moving classes to another pkg / fixing docs
* : reducing dependencies
* : reducing dependencies
* : fixed justCRLMM
* : fixing vignette and docs
* : fixing vignettes
* : fixing s4links - docs
* : fixing s4links - docs
* : Fixing justCRLMM/justSNPRMA for SNP 6.0 platform
* : fixing code to match docs
* : - The "db" generic has been renamed "dbconn" in
AnnotationDbi
so oligo must
define the "db" generic itself now. (Note that if this was
the
only reason
to make oligo depend on AnnotationDbi, then maybe this could
go
away now).
- Version bump.
oligoClasses
* : Adding oligoClasses
* : Adding oligoClasses
* : Fixing exported methods
* : export SnpLevelSet in NAMESPACE. changed setValidity
methods
for the SnpLevel classes
* : just bumping the version number -- forgot to do this with
the
last commit
* : started a few man pages
* : exposing required classes
* : bumped assayData accessors up to SnpLevelSet
* : preping for release
* : removed quotes surrounding linkS4Class{eSet}
* : adding docs
* : fixing missing links on docs
oneChannelGUI
* : Adding GO enrichment also to exon array data. The link to
GO
terms is done using the human/mouse/ratLLMapping libraries.
Exon analysis: Adding a filter to remove cross hybridizing
probe
sets on the basis of Affymetrix cross_hyb or xhyb annotation
fields
Exon analysis: Adding a revIQR filter that removes highly
variant
probe sets.
Exon analysis: Adding a average mean difference Splice Index
filter.
* : Vignette Revision.
Splice Index is non any more dependent by APT tools.
Splice Indexes inspection function was revised.
* : Updating the alternative splicing analysis example in
oneChannelGUI vignette.
Fixing a bug in MA plot QC
ontoTools
* : updated objects
OrderedList
* : fix an issue with as.logical on factors going crazy
M R/OrderedList.R
M DESCRIPTION
* : Diese und die folgenden Zeilen werden ignoriert --
M email adress updated
OutlierD
* : added the OutlierD package
Maintainer: Sukwoo Kim
pathRender
* : some visualization improvements, and possibility of
returning
the graph object
* : added ras pathway
* : saving while machines down
* : saving more code for expr graph plots
* : saving for now
* : drop plotExG.Rnw
* : moved out plotExG (error)
* : safe spot for plotExG fiddling
pcaMethods
* : Remove dependence on R without version specification
pdInfoBuilder
* : Fix broken collate field
* : Changing table name for SNP6 chips
* : Adding docs
* : Adding docs
* : Vince is now the maintainer of pdInfoBuilder
* : adding featureSet fsetid index
* : added pdBuilders in inst to save the key building exemplars
PGSEA
* : Edited PGSEA() so that it works with GeneSetCollections,
also
fixed appropriate help file
* : Minor vignette addition
* : Minor bug fix
* : Added VAI curated gene sets in GeneSetCollection format,
with
appropriate documentation and vignette changes...
* : Fixed nbEset - depreciated exprSet object
Added kegg2smc() and appropriate docs
pkgDepTools
* : Fix makeDepGraph to prevent addition of duplicate nodes
plateCore
* : Create dir for plateCore
* : Committing current version of my flowPlate package. Most
functions have annotation, but may things still depend on my
plate layout so they won't be terribly useful to others yet.
* : Committing sample plate description.
* : Made changes for validation report.
* : Initial import of Gosink methods
* : I'm adding a bunch of methods, some of which are for
general
use with flow
cytometry data, and others are specific for parsing flowJo
workspaces.
plgem
* : Updates, bug fixed and new function added on the
plgem_1.9.1
version:
-LPSeset.rda dataset has been updated from exprSet to
ExpressionSet class
-the requirement of the 'conditionName' covariate in the
phenoData of the ExpressionSet has been eliminated; now a
numeric
index (covariateNumb) needs to be provided to indicate which
covariate has to be used to identify the different
experimental
conditions and set of replicated arrays on the ExpressionSet
-functions and documentation updated based again on the
switch
from the exprSet to the ExpressionSet class and on the
addition
of the covariateNumb argument
-a new function plgem.write.summary has been added providing
a
simple wrapper for writing on the disk the list(s) of
differentially expressed genes
plier
* : <stdlib.h> is the standard, not <malloc.h>
* : changed Ts/Fs to TRUEs/FALSEs in justPlier
ppiStats
* : I have update the package so it passes check
* : added degreeEstimates functions and changed to version
1.3.10
* : forgot to add functions last time
prada
* : fixed bug in subsetting of cytoSets
* : tcltk is now in suggests and the progressbar function will
check for availability. If no tcltk is found it will exit
gracefully with a warning. No code should break by that
change,
the progress bar will simply not appear.
preprocessCore
* : more "R_rlm_interfaces.c" from affyPLM to preprocessCore
* : add additional shared include files
* : register two additonal functions
* : additional .h file
* : move log_median and median_log code from affyPLM to
preprocessCore
* : checkin missing header file
* : add R level interfaces for fitting a row-col effects model
(ala
RMA) to a user specified matrix
* : add colSummarize* functions
* : fix invalid returns in stub functions
* : add subColSummarize* functions
* : standardize all exported C level functionality
* : improved documentation
prism
* : Bumped for LazyLoad.
PROcess
* : Bumped for LazyLoad.
puma
* : lwd argument added to plotROC
* : new function numTP to calculate number of true positives
* : pumaComb now checks whether there is already an MPI cluster
before attempting to create a new one
* : pumaPCA now has a default sampleSize of 1000 as this makes
it
much quicker to run and generally gives similar results to
running on whole data set
* : create_eset_r now removes column names from exprs and
se.exprs
as this was causing errors due to changes made recently to
Biobase
* : bumped version number
* : Added documentation for numTP and bumped version number
* : Fixed bug that was causing pumaComb to fail if a snow
cluster
was used as an argument
* : Added fold change (FC) to DEResult object when using pumaDE
* : pumaClust: set default number of clusters to 10, and
enabled
the function to take an ExpressionSet or exprReslt object as
first argument
* : Created write.reslts methods for pumaPCARes and
ExpressionSet
classes
* : statistic and FC slots of DEResult class now matrix rather
than
data.frame
* : removed vignette source (puma.Rnw), as it now takes a long
time
to build the vignette. The pdf file for the vignette
(puma.pdf)
is still included
* : added an extra line (varLabels(affybatch.example) <-
c("level")) to many of examples in documentation to remove
errors
introduced recently from changes elsewhere (though not quite
sure
where these were introduced)
* : changed how the varLabels in the final ExpressionSet are
created to remove a bug recently introuced from elsewhere
(though
not quite sure where the bug was introduced from)
* : Made many changes to vignette including details of how to
write
results out to file at various stages, brief example of
pumaClust, example of using a remapped cdf and updated
(simpler)
details of how to get parallel functionality working.
Vignette
now only available as pdf file, but email maintainer if you'd
like the source code (puma.Rnw)
* : Bumped version number to 1.3.4
* : Changed default option of parallelCompute in pumaComb as
this
seemed to be causing things to fail on the build machine
(lamb1)
* : Fixed bug in createDesignMatrix that was causing errors in
ExpressionSets with non-informative factors
qvalue
* : fixed up a missing tcltk dependency
RbcBook1
* : Use new form of call to Biobase::cache()
RBGL
* : I fixed misspellings of "requires".
* : streamline sp.between and sp.between.scalar
* : more on sp.between/obsolete sp.between.scalar
* : add a few na.rm=TRUE in interfaces.R
* : better use of any-function in interfaces.R
* : clarification on kCores/sp.between
* : close connections explicitly in examples
* : close connections explicitly in vignette
RDocBook
* : caption handling protocol
* : minor change for italics
reb
* : Fixed a couple small errors...
* : Renamed a function to fix an S3/generic warning...
RefPlus
* : Added items remotely
D:\RefPlus\RefPlus_1.7.0\RefPlus\inst\doc\An Exploration of
Extensions to the RMA Algorithm.pdf
* : Added items remotely
D:\RefPlus\RefPlus_1.7.0\RefPlus\inst\doc\index.html
Resourcerer
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
rflowcyt
* : modif man page to remove warnings from check
* : Fix missing link in plotECDF.FCS doc
* : fix man page link for xyplot
Rgraphviz
* : change for graphviz 2.14 release
* : misc fixes in configure.in
* : adjust for graphviz-2.14.1 release
* : adjust for graphviz-2.14.1 release
* : Have configure try /usr/local as last attempt if no
--with-graphviz provided
When no configure arguments are provided, the script tries:
1. use pkg-config if available
2. use dotneato-config if available (this will only be
present
for
very old versions of graphviz)
3. use /usr/local. This allows us to build Rgraphviz without
specifying any configure args on OS X as part of our
automated
build process.
* : correct author
rhdf5
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
Ringo
* : modified asExprSet conversion function to accommodate
1-sample
MALists as well
* : slightly improved the auxiliary scripts makeProbeAnno.R and
graphPeaks2Transcripts.R
* : fixed bug in function chipAlongChrom that occurred if no
features were mapped to selected genomic region
* : replaced example data by official demo data provided by
NimbleGen
* : cosmetic corrections to the package vignette
* : minor clarifications to peak class objects and the
corresponding modifications; fixed example for preprocess
function
* : minor change to makeProbeAnno.R script for improved handling
of
variable probe-lengths
* : extended and clarified two sections of the vignette
* : removed deprecated function sliding.median that has been
replaced by the more general sliding.quantile
* : NaN -> NA_REAL in C code
Rintact
* : I have updated the packages to account for the two new
S4-classes intactGraph and intactHyperGraph. I have also
implemented the translateIntactID method for both these
classes
as well as its corresponding generic. I have also updated man
pages.
* : I have updated the namespace to export the initialize
method
* : I have updated the package so that the initialize method is
correct for intactHyperGraph
* : I have made some modifications to the function
intactXML2Graph.R
* : I have modified the parser to handle different
representations
of the xml files as they may differ
* : I have edited the vignette and added some accessor
functions. I
also
made the show methods a bit nicer.
* : I have updated the package to include some S4
documentation.
Further updates are coming
* : I have added the necessary man pages and modified
list2Matrix.
The modification to list2Matrix should also fix the problem
in
the vignette of ScISI
* : i have added two xml files as examples
* : I have created accessor functions and updated the man pages
and
Namespace
RMAGEML
* : not supported on Windows and Mac OS X (per Martin's
request)
* : oops
ROC
* : rationalized graphics -- plot, lines, points, ... handled
better
* : ansification by paul gordon of u calgary
* : ansification by paul gordon u calgary
rsbml
* : Added new contributed package rsbml
* : Tag windows and mac builds as not supported
* : Behind-the-scenes work towards support for libsbml 3.0
(upstream bugs
are blocking). Disable consistency checking to avoid bugs on
Windows.
* : Revert last change, forgot it added a lot of API, also get
rid
of
temporary build files.
* : Re-enable windows build system support
RSNPper
* : repairs to data.frame handling
Ruuid
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : Remove apparently unneeded dependencies on libg2c and
libRblas
on Windows
RWebServices
* : Maintainer field of Biocore Team packages now points to the
BioC List
Since biocpkgs at lists.fhcrc.org seems to be a spam magnet and
isn't
getting much, if any, use we are changing the maintainer
email
address
for BioC Core Team maintained packages to simply be the main
Bioconductor user email list. Most users report problems
there
anyhow
and we feel that encouraging that single channel for bug
reports
is
best.
* : not supported on Windows and Mac OS X (per Martin's
request)
SAGElyzer
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
* : To pass check in R-2.6.0
* : Remove stray brace in docs
SBMLR
* : updated
ScISI
* : Fix Depends, Imports, and NAMESPACE
Matrix was being used without being declared and it seems that
it
needs to be attached via Depends and not just imported in the
NAMESPACE. The env-API of AnnotationDbi is now imported in
the
NAMESPACE file.
* : I have updated the package so that it builds and checks
with
only one warning. The changes
have been incorporated to match the changes with
AnnotationDbi,
and Rintact, as well as
updated documentation.
* : I have updated the package so that it finally passes check
* : I have added two data files to update the vignettes and
increased the version number
* : I have created a new version of ScISIC
seqLogo
* : Now allowing plot axes to be customized to some extent
siggenes
* : Just a little bug fix.
* : And another little bug.
* : Enabled splitting of the data set in the categorical case
(if
approx = TRUE).
simpleaffy
* : added setAllQCProbes setAllSpikeProbes and setAlpha. Added
wheat to qc data tables
* : changes to underlying QC representation. Deprecated many QC
functions replaced with functions of the form qc.get. and
qc.set.
. Updates to the QC man pages and examples therein.
* : updated vignette, docs
* : fixed setMethod signature for plot.qc.stats
simulatorAPMS
* : I have updated the man pages so that the examples now work
properly
SMAP
* : Changed from uniform priors of transition and initial
probabilities to Dirichlet priors.
* : Changed to uniform Dirichlet priors for transition and
initial
probabilities. Corrected a bug in gradient.c. Improved the
modified Viterbi algorithm for overlap consideration.
snapCGH
* : changes to help files
* : speeding up some functions
* : More corrections
SNPchip
* : now depends on R 2.6 and oligo >= 1.1.5
* : Removed dependency on oligo. Functions copyNumber, calls,
etc.
defined in functions.R are temporary until the class
defitions
for SnpCallSet, SnpCopyNumberSet are ported to Biobase
* : numerous changes to the infrastructure
* : provided coercion methods for deprecated classes
* : bug fixes. changed unsplitS4 to unsplitSnpSet
* : bug fit to .drawYaxis
* : fixed plotCytoband bug. Changed definition of oligoSnpSet
class
* : restore default par settings after plotCytoband
* : added documentation for snpPar, sample.snpset
* : removed oligo from imports. Depends on oligoClasses
* : added .commands.R to data/
* : added another updateObject method for the deprecated
AnnotatedSnpSet class
* : fixed bug in .calculateYlim and .recycle
* : this is to bump the version number of my last bug fix
* : plotSnp is a method for SnpLevelSet
* : only print one.ylim message in getPar if the number of
panels
to plot is greater than 1
* : added classes for graphical parameters. Updated annotation
slot
in sample.snpset. Updated Vignette. Updated plotSnp methods.
Added documentation for newly defined classes
* : added getSnpAnnotation methods for oligoSnpSet, SnpCallSet,
and
SnpCopyNumberSet
* : added aliases for getSnpAnnotation
* : log option in plot added
splicegear
* : many fixes to accomodate changes (mostly in Biobase).
Still one warning remains.
This is probably the last release of this package.
splots
* : I updated the man page and user interface of the function,
and added the "main" and "na.fill" parameters.
* : fix typo in Author
* : bugfix: rgb does not like NA
* : truncate value to be within zrange before plotting
tilingArray
* : Added SessionInfo to end of vignettes
* : removed obsolete comment re "cache".
* : an updated version, run with current R 2.6 and current
packages
no substantial changes to content.
tkWidgets
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
* : Getting the package pass check under R-2.6.0
* : Just to pass check under R-2.6.0
* : License changed to Artistic.
* : fixed up brace mismatch in the man pages
topGO
* : Fixed compatibility with the new release of xtable package.
* : Fixed compatibility with the new release of xtable package.
* : * Replace annotate package with AnnotationDbi
* Cleaning the code
* : * Added high-level function run() for easily applying the
algorithms
Ex: > run(GOdata, algorithm = "elim", statistic = "KS")
* Function genTable() is now deprecated. It is replaced by
GenTable() which
takes as arguments topGOdata and topGOresult objects. The
user
can
specify one ore more topGOresult objects.
* The "alternative" parameter from classicScore class was
replaced with
scoreOrder which values can be either "increasing" or
"decreasing".
scoreOrder = "increasing" means that genes with lower score
are
more significant. For example, the p-value of a gene-wise
test
statistic. scoreOrder = "decreasing" means that genes with
larger
score are the interesting ones (the t-statistic of a gene in
case
we are interested in up-regulation).
* More code cleaning
twilight
* : fixed library.dynam
* : updated Rd files
* : repaired S3 method usage
* : eliminated multiple functions definitions
* : last changes
* : last changes to vignette
* : exchanged some German character
TypeInfo
* : Bumped for LazyLoad.
VanillaICE
* : added ICE package
* : renamed ICE package -> VanillaICE
Maintainer: Robert Scharpf
vbmp
* : This is meant to address points 1 and 2 raised by
Bioconductor
reviewers.
- The package now includes the BRCA12 dataset in
ExpressionSet
format.
- The vignette provides more details on the code. A second
example using BRCA12 dataset is included
* : Correction to the BRCA12 dataset information and to the
vignette
vsn
* : Removed two unused variable definitions.
* : more detail into man page about the AffyBatch method of
justvsn
* : Added ties.method="random" to the rank computation in
meanSdPlot
* : added a drop=FALSE in a matrix subset operation that should
always
result in matrix
* : I rationalized the relationship between vsn2 and justvsn,
and
started
updating the vignette section about NChannelSet and RGList
methods.
* : Now the vignette works again (after changes to justvsn
etc.)
* : Now vsn has a local copy of RGList -> NChannelSet coercion
method,
as advised by RG. The hack with the under-the-hood loading of
"convert" is gone. I also added a test that tries to make
sure
that
this oercion method is iddentical with that of the coerce
package.
* : minor improvements
* : rowV (which is also used by meanSdPlot) now uses (n-1) in
the
denominator of variance estimator rather than n
* : cosmetic betterments
* : Forget the stupid testing, it is just to complicated.
* : removed the postfixing of channelnames to colnames in
justvsn-NChannelSet
* : better validity checking of resulting objects
* : I rationalized the distribution of functionality between
the
functions
vsn2, predict and justvsn, and updated their documentation.
webbioc
* : Bumped for LazyLoad.
widgetInvoke
* : Bumped for LazyLoad.
widgetTools
* : On Robert's request, removed all notes from the man pages
that
were of the form:
\note{This function is part of the Bioconductor project at
Dana-Farber
Cancer Institute to provide Bioinfomatics functionalities
through
R.}
xcms
* : Fixed bug were fillPeaks() would fail if there was only one
peak to find
Made getPeaks() slightly more memory efficient by correcting
an
oversight
flush.console() is now called on all systems during long
operations
* : Making fillPeaks() robust for zero missing peaks as well
* : rawEIC uses binary search
findMZBoxes gives proper error messages
findPeaks.centWave
- new baseline and S/N estimation (default snthresh=20)
bugfix for MSW.getRidge
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