Entering edit mode
Mark Cowley
▴
910
@mark-cowley-2951
Last seen 9.6 years ago
Dear list,
Within the GSEABase package, there are various types of identifier
classes (eg GenenameIdentifier, EntrezIdentifier,...) and i'd like to
create a UniprotIdentifier, since it does not already exist, and
ultimately i'd like to convert between accession types using
org.Hs.eg.db and mapIdentifiers function.
Following the hint within GeneIdentifierType-class.Rd, i've added a
custom UniprotIdentifier class:
setClass("UniprotIdentifier",
contains="GeneIdentifierType",
prototype=prototype(
type=new("ScalarCharacter", "Uniprot")))
# but the default constructor in that hint is too simple & does not
support the annotation argument which is crucial for mapping between
GeneSet types:
UniprotIdentifier <- function() new("UniprotIdentifier")
UniprotIdentifier()
# geneIdType: Uniprot
# make a geneset
up <- c("Q9Y6Q1", "A6NJZ7", "Q9BXI6", "Q15035", "A1X283", "P55957")
gs <- GeneSet(up, geneIdType=UniprotIdentifier())
gs
# setName: NA
# geneIds: Q9Y6Q1, A6NJZ7, ..., P55957 (total: 6)
# geneIdType: Null
# collectionType: Null
# details: use 'details(object)'
# try to map to EntrezIdentifier
mapIdentifiers(gs, EntrezIdentifier())
Error in .mapIdentifiers_isMappable(from, to) :
unable to map from 'Uniprot' to 'EntrezId'
neither GeneIdentifierType has annotation
Given that the GenenameIdentifier constructor looks like this:
GenenameIdentifier <- function (annotation, ...) {
args <- names(match.call())[-1]
GSEABase:::.checkRequired(NULL, args)
miss <- "annotation"[!"annotation" %in% args]
oargs <- list(annotation = annotation, ... = ...)[!names(list(
annotation = annotation, ... = ...)) %in% miss]
do.call(new, c("GenenameIdentifier", oargs))
}
# <environment: 0x1052a1308="">
GenenameIdentifier()
# geneIdType: Genename
# why does my constructor not work?
UniprotIdentifier <- function (annotation, ...) {
args <- names(match.call())[-1]
GSEABase:::.checkRequired(NULL, args)
miss <- "annotation"[!"annotation" %in% args]
oargs <- list(annotation = annotation, ... = ...)[!names(list(
annotation = annotation, ... = ...)) %in% miss]
do.call(new, c("UniprotIdentifier", oargs))
}
UniprotIdentifier()
# Error in list(annotation = annotation, ... = ...) :
# 'annotation' is missing
# FYI: Here's a constructor that does work, but it's a lot different
to the ones provided by GSEABase class.
UniprotIdentifier <- function (annotation, ...) {
args <- names(match.call())[-1]
oargs <- if(missing(annotation)) list(... = ...) else
list(annotation = annotation, ... = ...)
do.call(new, c("UniprotIdentifier", oargs))
}
UniprotIdentifier()
# geneIdType: Uniprot
UniprotIdentifier(annotation="org.Hs.eg.db")
# geneIdType: Uniprot (org.Hs.eg.db)
# With that final constructor, I can now convert from UniProt Id's to
other types of ID:
gs <- GeneSet(up)
geneIdType(gs) <- UniprotIdentifier()
gs <- GeneSet(up, geneIdType=UniprotIdentifier())
gs <- GeneSet(up,
geneIdType=UniprotIdentifier(annotation="org.Hs.eg.db"),
setName="testA")
mapIdentifiers(gs, EntrezIdentifier())
# setName: testA
# geneIds: 827, 83874, ..., 637 (total: 5)
# geneIdType: EntrezId (org.Hs.eg.db)
# collectionType: Null
# details: use 'details(object)'
cheers,
Mark
-----------------------------------------------------
Mark Cowley, PhD
Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------
sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu95av2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4
[4] DBI_0.2-5 GSEABase_1.12.2-1 graph_1.28.0
[7] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0
loaded via a namespace (and not attached):
[1] tools_2.12.2 XML_3.2-0 xtable_1.5-6
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