reRank {RcisTarget} | R Documentation

## 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, 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)

[Package RcisTarget version 1.10.0 Index]