reRank: Re-rank RcisTarget ranking

In RcisTarget: RcisTarget: Identify transcription factor binding motifs enriched on a gene list

Description

Re-ranks the genes/regions in the database for each motif. This allows to do motif enrichment over a background.

Usage

reRank(rankingsDb, columns = NULL, indexCol = "features")

Arguments

rankingsDb	Results from RcisTarget (data.table)
columns	Whether to add the HTML tag <img> around the URL or not (boolean).
indexCol	Name of the column (in the ranking) which contains the motif/feature ID.

Value

Returns a new ranking database with the new ranking values.

See Also

See the "background" vignette for more examples: vignette("RcisTarget-withBackground")

Examples

library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)
data(hg19_500bpUpstream_motifRanking_cispbOnly)
motifRankings <- hg19_500bpUpstream_motifRanking_cispbOnly


genes <- colnames(getRanking(motifRankings))[10:20]
reRank(motifRankings, columns=genes)

RcisTarget documentation built on Nov. 8, 2020, 6:57 p.m.