getREACTOMEPATHTerms: Get Pathway names of given REACTOME PATH_DB IDs

In GeneAnswers: Integrated Interpretation of Genes

Description

Function to map given REACTOME PATH_DB IDs to Pathway names.

Usage

getREACTOMEPATHTerms(pathIDs, allowNA=TRUE)

Arguments

pathIDs	a REACTOME PATHWAY IDs vector
allowNA	logic, to determine whether change unrecognized term names or not

Value

return a REACTOME pathway terms of given REACTOME PATH_DB IDs. If the REACTOME service is not available, the function will stop.

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

Examples

## Not run: getREACTOMEPATHTerms(c('174143', '453274'))

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

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    union

Loading required package: RCurl
Loading required package: bitops
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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, 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, cbind, colMeans, colSums, colnames, 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
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Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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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' 

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