Dump Jaspar motifs into a HOMER motif file.

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

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")))
#> [1] TRUE