reRank: Re-rank RcisTarget ranking

Description Usage Arguments Value See Also Examples

View source: R/aux_reRank.R

Description

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

Usage

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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

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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 April 21, 2021, 9:46 a.m.