expect_equal for comparing
numerical valuesTransformCatalog in case R was
configured and built in a way that did not support long double.Updated documentation of ReadCatalog and
ReadCatalogInternal as there are no ID96 catalogs in COSMIC
v3.2.
Changed the URL of COSMIC mutational signatures page to the redirected URL.
Updated some tests for TransformCatalog in case R
was configured and built in a way that did not support long
double.
Added the argument strict back to
ReadCatalog for backward compatibility; strict
is now ignored and deprecated.
Robustified function StandardChromNameNew to select
the column which contains chromosome names by name instead of column
index.
Fixed a bug in function
CheckSeqContextInVCF.
Fixed a bug in function PlotCatalog.SBS96Catalog
when plotting the X axis after setting
par(tck) = 0.
Changed PlotCatalog to round the mutation counts for
each main type for SBS96, SBS192, DBS78 and ID counts catalog in case
the input is reconstructed counts catalog.
Updated function AdjustNumberOfCores not to throw a
message on MS Windows machine.
Added an additional argument ylabels to
PlotCatalog and PlotCatalogToPdf. When
ylabels = FALSE, don’t plot the y axis labels. Implemented
for SBS96Catalog, DBS78Catalog, IndelCatalog.
Enabled argument grid, uppder,
xlabels in PlotCatalog and
PlotCatalogToPdf for DBS78Catalog, IndelCatalog.
ReadCatalog to import files with:
ReadCatalog function,
e.g. ReadCatalog.SBS96Catalog. Now they are in
data-raw/obsolete-files/ReadCatalogMethods.R.ConvCatalogToICAMS to convert
SigProfiler/COSMIC-formatted catalog files into ICAMS catalog objects.
Now these functions are in
data-raw/obsolete-files/ConvCatalogToICAMS.R, and their
functionalities are integrated into ReadCatalog.ReadCatalog to remove rows which
have NA in the data table read in. Otherwise the number of rows will not
be accurate to infer the correct catalog type.InferClassOfCatalogForRead to
data-raw/obsolete-files/InferClassOfCatalogForRead.R.CreateOneColDBSMatrix when
returning 1-column DBS144 matrix with all values being 0 and the correct
row labels.Added an additional argument tmpdir in function
AddRunInformation.
Updated function CheckAndRemoveDiscardedVariants and
MakeDataFrameFromVCF to check for variants that have same
REF and ALT.
Create new temp directory when generating zip archive from VCFs to avoid zipping unnecessary files in the output.
Fixed a bug in function AddRunInformation for
allowing ref.genome to be a Bioconductor package.
Fixed bugs in function CreateOneColSBSMatrix,
CreateOneColDBSMatrix and CreateOneColIDMatrix
when the variants in the input vcfs should all be discarded.
Updated function CheckAndFixChrNames to give a
warning instead of an error when “23” and “X” or “24” and “Y” appear on
the chromosome names on the VCF at the same time.
CheckAndFixChrNames will change “23” to “X” or “24” to “Y”
internally for downstream processing.
Changed some code in function AddTranscript,
CreateOneColSBSMatrix, CreateOneColDBSMatrix
to use functions from package dplyr instead of
data.table due to segfault error.
RemoveRowsWithDuplicatedCHROMAndPOSNew
to remove variants that have same CHROM, POS, REF.files in function
VCFsToZipFile.Fixed a bug in ReadAndSplitVCFs for merging adjacent
SBSs into DBS when variant.caller is
mutect.
Fixed a bug inCheckAndRemoveDiscardedVariants for
removing wrong DBS variants.
CheckAndRemoveDiscardedVariants to
remove wrong DBS variants that have same base in the same position in
REF and ALT (e.g. TA > TT or GT > CT).name.of.VCF in function
MakeDataFrameFromVCF for better error reporting.Updated function MakeDataFrameFromVCF for better
error reporting when reading in files that are actually not
VCFs.
Updated function ReadVCFs to automatically change
the number of cores to 1 on Windows instead of throwing an
error.
CheckAndFixChrNames for returning the
correct number of chromosome names.stop.on.error and code
tryCatch in function VCFsToCatalogs for better
tracing if the function stops on error.Added argument stop.on.error to
VCFsToCatalogs; if false, return list with single element
named error.
Added new internal function
CheckAndFixChrNamesForTransRanges. The chromosome names in
exported data TranscriptRanges don’t have “chr”. ICAMS now
will check for the chromosome names format in input vcf and update the
trans.ranges chromosome names in function AddTranscript if
needed.
Added new argument name.of.VCF in function
AnnotateSBSVCF and AnnotateDBSVCF for better
error reporting.
Changed return from ReadCatalog to include possible
attribute “error” and allow for not calling stop() on error.
For a stranded catalog, as.catalog and
ReadCatalog will silently convert region = “genome” to
“transcript”.
Updated function AddTranscript to check whether the
format of VCF chromosome names is consistent with that in
trans.ranges used.
Removed documentation warnings related to
Some file reorganization.
CreateOneColSBSMatrix for showing
message that SBS variant whose reference base in ref.genome does not
match the reference base in the VCF file.Enabled functions PlotCatalog and
PlotCatalogToPdf to plot a numeric matrix, numeric
data.frame, or a vector denoting the mutation
counts.
Added new internal function AdjustNumberOfCores to
change the number of cores automatically to 1 if the operating system is
Windows.
Added test processing VCF with unknown variant caller.
Added new internal function SplitSBSVCF,
SplitOneVCF, SplitListOfVCFs and
VCFsToZipFileXtra, WriteSBS96CatalogAsTsv,
ReadSBS96CatalogFromTsv,
GetConsensusVAF.
Added new exported function
ReadAndSplitVCFs, VCFsToCatalogs,
VCFsToCatalogsAndPlotToPdf and
VCFsToZipFile.
Added new argument filter.status and
get.vaf.function in functions ReadVCF,
ReadVCFs, ReadAndSplitVCFs,
VCFsToCatalogs, VCFsToCatalogsAndPlotToPdf and
VCFsToZipFile.
Added a new internal data
catalog.row.headers.SBS.96.v1.
Added new argument max.vaf.diff in internal
functions SplitOneVCF, SplitListOfVCFs and
exported functions ReadAndSplitVCFs,
VCFsToCatalogs, VCFsToCatalogsAndPlotToPdf and
VCFsToZipFile.
Added new dependency package parallel.
Added new dependency package R.utils for
data.table::fread to read gz and bz2 files
directly.
Added new argument num.of.cores in internal
functions ReadVCFs, SplitListOfVCFs and
exported functions ReadAndSplitVCFs,
VCFsToCatalogsAndPlotToPdf, VCFsToCatalogs,
VCFsToZipFile, VCFsToIDCatalogs,
VCFsToSBSCatalogs, VCFsToDBSCatalogs.
Added new argument ... in internal functions
ReadVCF, ReadVCFs and exported functions
ReadAndSplitVCFs, VCFsToCatalogsAndPlotToPdf,
VCFsToCatalogs, VCFsToZipFile.
Added new argument mc.cores in internal functions
GetConsensusVAF.
MakeDataFrameFromVCF to use
data.table::fread instead of read.csv.MakeDataFrameFromVCF when reading in VCF
from URL.Updated function CreateOneColSBSMatrix to throw a
message instead of an error when there are SBS variant whose reference
base in ref.genome does not match the reference base in the VCF
file.
Updated function MakeVCFDBSdf to inherit column
information from original SBS VCF.
Changed the words in legend for DBS144 plot from “Transcribed”, “Untranscribed” to “Transcribed strand” and “Untranscribed strand”.
Updated the documentation for exported data all.abundance.
Updated function ReadCatalog.COMPOSITECatalog not to
convert “::” to “..” in the column names.
Updated various functions in ICAMS to generate catalogs with zero mutation counts from empty vcfs.
Added a section “ID classification” in the documentation for
exported data catalog.row.order.
New argument suppress.discarded.variants.warnings in
exported function AnnotateIDVCF with default value
TRUE.
Added another paper information in
AddRunInformation. “Characterization of
colibactin-associated mutational signature in an Asian oral squamous
cell carcinoma and in other mucosal tumor types”, Genome Research 2020
https://doi.org/10.1101/gr.255620.119.
Changed the format of DOIs in DESCRIPTION according to CRAN policy.
Changed back the return value of ReadStrelkaIDVCFs,
ReadStrelkaSBSVCFs, ReadMutectVCFs to a list
of data frames with no variants discarded.
Combined all the discarded variants from
ReadAndSplitMutectVCFs and
ReadAndSplitStrelkaSBSVCFs under one element
discarded.variants in the return value. An extra column
discarded.reason were added to show the details.
Updated internal functions ReadVCF and
ReadVCFs not to remove any discarded variants.
No more removal of “chr” in the CHROM column when
reading in VCFs.
CheckAndReturnSBSMatrix,
CheckAndReturnDBSMatrix,
CreateOneColSBSMatrix,CreateOneColDBSMatrix,
VCFsToSBSCatalogs, VCFsToDBSCatalogs.CalculateExpressionLevel for the edge
case.CreateOneColIDMatrix when the ID.class
contains non canonical representation of the ID mutation type.The return value of exported function
ReadStrelkaIDVCFs now sometimes contains a new element,
discarded.variants. This appears when there are variants
that were discarded immediately after reading in the VCFs. At present
these are variants that have duplicated chromosome/positions and
variants that have illegal chromosome names. This means that the user
must check the return to see if discarded.variants is
present and remove it before passing the return to a function that
expects a list of VCFs. Code in ICAMS that takes lists of VCFs already
checks for this element and removes it if present.
Added argument return.annotated.vcfs to
exported function VCFsToIDCatalogs. The default
value for the argument is FALSE to be consistent with
other functions.
Argument return.annotated.vcfs in functions
VCFsToSBSCatalogs,VCFsToDBSCatalogs,
VCFsToIDCatalogs, MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf,
MutectVCFFilesToZipFile,
StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf,
StrelkaSBSVCFFilesToZipFile,
StrelkaIDVCFFilesToCatalog,
StrelkaIDVCFFilesToCatalogAndPlotToPdf and
StrelkaIDVCFFilesToZipFile.
Argument suppress.discarded.variants.warnings in
functions ReadAndSplitMutectVCFs,
ReadAndSplitStrelkaSBSVCFs,
VCFsToSBSCatalogs,VCFsToDBSCatalogs,
VCFsToIDCatalogs, MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf,
MutectVCFFilesToZipFile,
StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf,
StrelkaSBSVCFFilesToZipFile,
StrelkaIDVCFFilesToCatalog,
StrelkaIDVCFFilesToCatalogAndPlotToPdf and
StrelkaIDVCFFilesToZipFile.
Added documentation to exported functions
ReadAndSplitStrelkaSBSVCFs,
StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf and
StrelkaSBSVCFFilesToZipFile.
Added information on the “ID classification” in documentation of
functions generating ID catalogs, FindDelMH and
FindMaxRepeatDel.
Minor changes to documentation of functions
PlotCatalog, PlotCatalogToPdf,
StrelkaSBSVCFFilesToZipFile,
StrelkaIDVCFFilesToZipFile and
MutectVCFFilesToZipFile.
Updated documentation for the return value of functions
StrelkaIDVCFFilesToCatalog,
StrelkaIDVCFFilesToCatalogAndPlotToPdf,
StrelkaIDVCFFilesToZipFile and
VCFsToIDCatalogs to make it clearer to the user.
Added new exported data of catalog row order for SBS96, SBS1536
and DBS78 in SigProfiler format to
catalog.row.order.sp.
New internal function
ConvertICAMSCatalogToSigProSBS96, ReadVCF,
ReadVCFs.
New exported function GetFreebayesVAF for
calculating variant allele frequencies from Freebayes VCF.
New test data for Strelka mixed VCF.
Added time zone information to file “run-information.txt” when
calling functions MutectVCFFilesToZipFile,
StrelkaSBSVCFFilesToZipFile and
StrelkaIDVCFFilesToZipFile.
Enabled “counts” -> “counts.signature” catalog transformation when the source catalog has NULL abundance.
Added legend for SBS192 plot and changed the legend text for SBS12 plot.
Added a second element plot.object to the return
list from function PlotCatalog for catalog types
“SBS192Catalog”, “DBS78Catalog”, “DBS144Catalog” and “IndelCatalog”. The
second element is a numeric vector giving the coordinates of the bar
midpoints, useful for adding to the graph.
Made the returns from PlotCatalog and
PlotCatalogToPdf invisible.
Improved time performance of GetMutectVAF,
CanonicalizeDBS, CanonicalizeQUAD.
if statements in GetCustomKmerCounts、
GetStrandedKmerCounts and
GetGenomeKmerCounts.
CreateOneColIDMatrix when there is NA ID
category.
GetMutectVAF to check if the VCF is indeed a Mutect
VCF.
CreateOneColDBSMatrix when the VCF does not have any
variant in the transcribed region.
CalculatePValues when there is only a single
expression value.
Created an internal function MakeDataFrameFromVCF to
read in data lines of a VCF.
New argument name.of.VCF in internal function
CheckAndFixChrNames to make the error message more
informative.
New argument name.of.VCF in exported
function AnnotateIDVCF to make the error message more
informative.
ReadStrelkaIDVCF to make the
error message more informative.AnnotateIDVCF to a list. The
first element annotated.vcf contains the annotated VCF. If
there are rows that are discarded, the function will generate a warning
and a second element discarded.variants will be included in
the returned list.flag.mismatches deprecated in
exported function AnnotateIDVCF. If there are
mismatches to references, the function will automatically discard these
rows. User can refer to the element discarded.variants in
the return value for the discarded variants.SplitStrelkaSBSVCF
when there are no non.SBS mutations in the input.MakeDataFrameFromMutectVCF when a Mutect VCF has no
meta-information lines.CreateOneColSBSMatrix
when an annotated SBS VCF has variants on transcribed regions that
all fall on transcripts on both
strand.CreateOneColDBSMatrix
when an annotated DBS VCF has variants on transcribed regions that
all fall on transcripts on both
strand.ReadAndSplitStrelkaSBSVCFs.MutectVCFFilesToZipFile,
StrelkaSBSVCFFilesToZipFile and
StrelkaIDVCFFilesToZipFile.trans.ranges to make it optional.name.of.VCF in internal
functions ReadStrelkaSBSVCF, ReadStrelkaIDVCF
and exported function GetStrelkaVAF.flag.mismatches in functions
VCFsToIDCatalogs, MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf,
MutectVCFFilesToZipFile,
StrelkaIDVCFFilesToCatalog,
StrelkaIDVCFFilesToCatalogAndPlotToPdf and
StrelkaIDVCFFilesToZipFile.GetStrelkaVAF andGetMutectVAF to a data frame which contains the VAF and
read depth information.PlotCatalogToPdf a list. The first element is a
logical value indicating whether the plot is successful. The second
element is a list containing the strand bias statistics (only for
SBS192Catalog with “counts” catalog.type and non-NULL abundance and
argument plot.SBS12 = TRUE).PlotCatalog and
PlotCatalogToPdf: For class SBS96Catalog:
(New) Allow setting ylim and cex.
(New) For PlotCatalog (not
PlotCatalogToPdf), allow plotting of a 96 x 2 catalog, in
which case behavior is a stacked bar chart. (New) Plot
x axis tick marks if xlabels is not TRUE; set
par(tck = 0) to suppress. For class IndelCatalog:
(New) Allow setting ylim.GetCustomKmerCounts.PlotTransBiasGeneExpToPdf so that ymax
on the plot will be changed based on plot.type.flat.abundance from “numeric” to “integer”.TransformCatalog; see documentation for rationale.TransformCatalog and updated
its documentation for parameter target.abundance.CheckAndFixChrNames and
updated the automated tests.TransformCatalog.GetMutectVAF
and updated the warning message to make it more informative.cbind to check the attributes of the incoming
catalogs and assign attributes accordingly.TransformCatalog to check the
attributes of the catalog to be transformed in the first place.AnnotateSBSVCF,
AnnotateDBSVCF and AnnotateIDVCF.PlotTransBiasGeneExp and
PlotTransBiasGeneExpToPdf.names.of.VCFs in
functions ReadAndSplitMutectVCFs,
ReadAndSplitStrelkaSBSVCFs, ReadStrelkaIDVCFs,
MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf,
StrelkaIDVCFFilesToCatalog,
StrelkaIDVCFFilesToCatalogAndPlotToPdf,
StrelkaSBSVCFFilesToCatalog and
StrelkaSBSVCFFilesToCatalogAndPlotToPdf for users to
specify the names of samples in the VCF files.as.catalog.gene.expression.data.HepG2 and
gene.expression.data.MCF10A.tumor.col.names
in functions ReadAndSplitMutectVCFs,
MutectVCFFilesToCatalog and
MutectVCFFilesToCatalogAndPlotToPdf to specify the column
of the VCF that contains sequencing statistics such as sequencing depth;
this column is often called “unknown” in Mutect.MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf,
StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf,
VCFsToSBSCatalogs, VCFsToDBSCatalogs,
ReadCatalog informing the user how to change attributes of
the generated catalog.VCFsToIDCatalogs,
StrelkaIDVCFFilesToCatalog and
StrelkaIDVCFFilesToCatalogAndPlotToPdf a list; 1st element
is the spectrum catalog (previously the only return); 2nd element is a
list of VCFs with additional annotations.PlotCatalog a list. The first element is a logical
value indicating whether the plot is successful. The second element is a
numeric vector giving the coordinates of all the bar midpoints drawn,
useful for adding to the graph (only implemented for SBS96Catalog).output.file argument in
MutectVCFFilesToCatalogAndPlotToPdf,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf, and
StrelkaIDVCFFilesToCatalogAndPlotToPdf so that an indicator
of the catalog type plus “.pdf” is simply appended to the base
output.file name. Also made this argument optional with
sensible default behavior.trans.ranges.GRCh37, trans.ranges.GRCh38 and
trans.ranges.GRCm38.FindDelMH, cryptic repeats (i.e. un-normalized
deletions in a repeat such as GAGG deleted from CCCAGGGAGGGTCCC, which
should be normalized to a deletion of AGGG) are now ignored with a
warning rather than causing a stop.FindDelMH, which
previously did not flag the cryptic repeat in what is now the second
example in the function documentation.as.catalog supports creation of the catalog from a
vector (interpreted as a 1-column matrix) and optionally infers the
class from the number of rows in the input.