reRank: Re-rank RcisTarget ranking

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Re-rank RcisTarget ranking

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)

Arguments

rankingsDb	Results from RcisTarget (data.table)
columns	Whether to add the HTML tag <img> around the URL or not (boolean).

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)

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.