motifToGene: motifToGene

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

Description

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

Usage

## S4 method for signature 'MotifList'
motifToGene(object, motifs, source)

Arguments

object	a MotifList object.
motifs	a character string
source	a character string, either 'MotifDb' or "TFclass' (case insensitive)

Value

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

Author(s)

Paul Shannon

See Also

MotifDb, geneToMotif, associateTranscriptionFactors, subset, query

Examples

  motifs <- c("MA0592.2", "ELF1.SwissRegulon", "UP00022")
  motifToGene(MotifDb, motifs, source="TFClass")
  motifToGene(MotifDb, motifs, source="MotifDb")

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