[BioC] Re: MetaData 1.6.0
jzhang at jimmy.harvard.edu
Fri May 21 17:45:11 CEST 2004
The developmental version of annotation packages (1.6.0) is now available and
can be accessed by doing (using hgu95av2 as an example):
> install.packages2("hgu95av2", develOK = TRUE)
The following changes/additions have been made:
a. Environments pkgNameNM and pkgNameNP (e. g. hgu95av2NM) no
longer exist in the platform specific packages
(e. g. hgu95av2) but are replaced by a new environment
pkgNameREFSEQ that contains the annotation data for all the
RefSeq accession records.
The environment pkgNameHGID has been droped. Mappings between
probe ids to HGID can be obtained through the mappings to LocusLink ids
to HGIDs in the homology data package.
b. GO package contains new environments ANCESTOR and OFFSPRING
that maps GO ids to all the ancestor and offspring along the
GO tree. GOTERM no longer exists and is replaced by GOTERMS
that maps GO ids to GOTerms objects with a GOId, Ontology
(originally in GOTERM), Synonym, Secondary, Definition, and
c. homology package now maps internal HomoloGeneIds to homoData
objects that has slots for organism name, LocusLink ids,
internal HomoloGeneIds, GenBack Accession numbers, type of
similarities, percent of identity, and urls for homologous
genes in other organism. Environment LL2HGID maps LocusLink
ids to internal HomoloGeneIds.
d. New annotation data packages for non-Affymetrix chips have
been added. These packages include hguMWG30kA, hguMWG30kB,
mguAtlas5k mguG4104A, mguG4120A, mguG4121A, mguMWG30kA,
mguMWG30kB, rguAtlas5k, rguG4105A, rguG4130A, rguMWG10k,
rguMWG5k. Pakckages with Atlas as part of the names are for BD
Biosciences microarrays, MWG for MWGAG BIOTECH microarrays, and G
for Agilent microarrays.
Due to the changes in data structure and contents, some environments of the
data packages in 1.6.0 may not be compatible with the libraries in Bioconductor
Comments/bug reports are welcome.
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