Description Usage Arguments Details Value Author(s) References See Also Examples
Function to retrieve KEGG category IDs containing given genes.
1 | getPATHList(geneVector, lib)
|
geneVector |
an Entrez gene IDs vector |
lib |
annotation library to be used to retrieve KEGG IDs. |
The current version only supports Bioconductor team maintained annotation libraries, like 'org.Bt.eg.db', 'org.Ce.eg.db', 'org.Cf.eg.edu', 'org.Dm.eg.db', 'org.Dr.eg.db', 'org.EcK12.eg.db', 'org.EcSakai.eg.db', 'org.Gg.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Rn.eg.db' and 'org.Ss.eg.db'.
return a KEGG genes ID list, names of the list are KEGG IDs and elements are genes IDs.
Gang Feng, Pan Du and Simon Lin
Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10
1 2 | a <- getPATHList(c('56458', '16590'), 'org.Mm.eg.db')
length(a)
|
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:igraph':
normalize, path, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
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'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: XML
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Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:AnnotationDbi':
select
Loading required package: Heatplus
Loading required package: RColorBrewer
Warning messages:
1: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
2: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Loading required package: org.Mm.eg.db
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