geneToMotif: geneToMotif

In MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs

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")

MotifDb documentation built on Nov. 8, 2020, 6:28 p.m.