write_transfac: Export motifs in TRANSFAC format.

In bjmt/universalmotif: Import, Modify, and Export Motifs with R

Export motifs in TRANSFAC format.

Description

Convert motifs to TRANSFAC format and write to file.

Usage

write_transfac(motifs, file, overwrite = FALSE, append = FALSE,
  name.tag = "ID", altname.tag = "NA")

Arguments

motifs	See convert_motifs() for acceptable formats.
file	character(1) File name.
overwrite	logical(1) Overwrite existing file.
append	logical(1) Add to an existing file.
name.tag	character(1) The tag to use when writing the motifs name slot.
altname.tag	character(1) The tag to use when writing the motifs altname slot. Note that no tag will be written if the slot is empty.

Details

If the family slot of a motif is not empty, then its contents will included using the HC tag. Similarly for the organism slot using the tag OS. The default name and alternate name tags are ID and NA, respectively, though these can be set manually.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

References

Wingender E, Dietze P, Karas H, Knuppel R (1996). “TRANSFAC: A Database on Transcription Factors and Their DNA Binding Sites.” Nucleic Acids Research, 24, 238-241.

See Also

read_transfac()

Other write_motifs: write_homer(), write_jaspar(), write_matrix(), write_meme(), write_motifs()

Examples

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                    package = "universalmotif"))
write_transfac(jaspar, tempfile())

bjmt/universalmotif documentation built on Nov. 16, 2024, 7:38 a.m.