mapIdsList: Effeciently converts collection of pathways using...

In fgsea: Fast Gene Set Enrichment Analysis

Description

Effeciently converts collection of pathways using AnnotationDbi::mapIds function. Parameters are the sames as for mapIds except for keys, which is assumed to be a list of vectors.

Usage

mapIdsList(x, keys, column, keytype, ...)

Arguments

x	the AnnotationDb object. But in practice this will mean an object derived from an AnnotationDb object such as a OrgDb or ChipDb object.
keys	a list of vectors with gene ids
column	the column to search on
keytype	the keytype that matches the keys used
...	other parameters passed to AnnotationDbi::mapIds

See Also

AnnotationDbi::mapIds

Examples

library(org.Mm.eg.db)
data(exampleRanks)
fgseaRes <- fgsea(examplePathways, exampleRanks, maxSize=500, eps=1e-4)
fgseaRes[, leadingEdge := mapIdsList(org.Mm.eg.db, keys=leadingEdge, column="SYMBOL", keytype="ENTREZID")]

Example output

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:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, 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


sh: 1: wc: Permission denied
Warning message:
In fgseaMultilevel(...) :
  For some pathways, in reality P-values are less than 1e-04. You can set the `eps` argument to zero for better estimation.
'select()' returned 1:1 mapping between keys and columns

fgsea documentation built on Nov. 8, 2020, 5:22 p.m.