geneToMotif {MotifDb} | R Documentation

## geneToMotif

### Description

Using either of our two sources ("MotifDb" or "TFClass") retrieve the names of the transcription factor binding motifs associated with the gene symbol for each transcription factor. Slightly different information is returned in each case but the columns "geneSymbol", "motif", "pubmedID", "source" are returned by both sources. The TFClass source is described here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383905/. The MotifDb source is in fact the usually 1:1 gene/motif mapping provided by each of the data sources upon which MotifDb is built.

### Usage

    ## S4 method for signature 'MotifList'
    geneToMotif(object, geneSymbols, source, ignore.case)

### Arguments

`object` | a `MotifList` object.
`geneSymbols` | a `character` string
`source` | a `character` string, either 'MotifDb' or 'TFclass' (case insensitive)
`ignore.case` | a `logical` variable, default FALSE, guiding gene name matching

### Value

A data.frame with these columns: geneSymbol, motif, pubmedID, source. The MotifDb source alos include dataSource and organism.

### Author(s)

Paul Shannon

### See Also

MotifDb, motifToGene, associateTranscriptionFactors, subset, query

### Examples

      genes <- c("ATF5", "FOS")
      geneToMotif(MotifDb, genes, source="TFClass")
      geneToMotif(MotifDb, genes, source="MotifDb")

[Package MotifDb version 1.22.0 Index]