fgsea: mapIdsList – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

mapIdsList

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.

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

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")]

fgsea

Fast Gene Set Enrichment Analysis

v1.16.0

MIT + file LICENCE

Authors

Gennady Korotkevich [aut], Vladimir Sukhov [aut], Nikolay Budin [ctb], Alexey Sergushichev [aut, cre]

Initial release