dumpJaspar: Dump Jaspar motifs into a HOMER motif file.

In fmicompbio/monaLisa: Binned Motif Enrichment Analysis and Visualization

Dump Jaspar motifs into a HOMER motif file.

Description

Get motifs from a Jaspar database package (e.g. JASPAR2020) and write them into a HOMER-compatible motif file as positional probability matrices.

Usage

dumpJaspar(
  filename,
  pkg = "JASPAR2020",
  opts = list(tax_group = "vertebrates"),
  pseudocount = 1,
  relScoreCutoff = 0.8,
  verbose = FALSE
)

Arguments

filename	Name of the output file to be created.
pkg	Name of the Jaspar package to use (default: JASPAR2020).
opts	A list with search options used in getMatrixSet. By default, only vertebrate motifs are included in the output using opts = list(tax_group = "vertebrates").
pseudocount	A numerical scalar with the pseudocount to be added to each element of the position frequency matrix extracted from Jaspar, before its conversion to a position probability matrix (default: 1.0).
relScoreCutoff	Currently ignored. numeric(1) in [0,1] that sets the default motif log-odds score cutof to relScoreCutoff * maximal score for each PWM (default: 0.8).
verbose	A logical scalar. If TRUE, print progress messages.

Value

TRUE if successful.

See Also

getMatrixSet for details on the argument opts. homerToPFMatrixList to read a file with HOMER-formatted motifs into a PFMatrixList.

Examples

dumpJaspar(filename = tempfile(), pkg = "JASPAR2020",
           opts = list(ID = c("MA0006.1")))

fmicompbio/monaLisa documentation built on Nov. 2, 2024, 1:33 p.m.