getPATHList: Retrieve KEGG categories containing given genes

In GeneAnswers: Integrated Interpretation of Genes

Description

Function to retrieve KEGG category IDs containing given genes.

Usage

getPATHList(geneVector, lib)

Arguments

geneVector	an Entrez gene IDs vector
lib	annotation library to be used to retrieve KEGG IDs.

Details

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'.

Value

return a KEGG genes ID list, names of the list are KEGG IDs and elements are genes IDs.

Author(s)

Gang Feng, Pan Du and Simon Lin

References

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

See Also

getCategoryList

Examples

a <- getPATHList(c('56458', '16590'), 'org.Mm.eg.db')
length(a)

Example output

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
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    '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
Loading required package: RSQLite
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

[1] 8

GeneAnswers documentation built on Nov. 8, 2020, 4:53 p.m.