read_transfac: Import TRANSFAC motifs.

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

Import TRANSFAC motifs.

Description

Import TRANSFAC formatted motifs. Assumed to be DNA motifs, type PCM. See system.file("extdata", "transfac.txt", pacakge="universalmotif") for an example motif.

Usage

read_transfac(file, skip = 0)

Arguments

file	character(1) File name.
skip	numeric(1) If not zero, will skip however many desired lines in the file before starting to read.

Details

A few TRANSFAC tags are recognized, including AC, ID, NA, HC and OS. HC will be set to the family slot and OS to the organism slot. If AC, ID and NA are present, then AC will be set as the motif name and NA as the alternate name. If AC is absent, then ID is set as the name. If ID is also absent, then NA is set as the motif name.

Value

list universalmotif objects.

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

Other read_motifs: read_cisbp(), read_homer(), read_jaspar(), read_matrix(), read_meme(), read_motifs(), read_uniprobe()

Examples

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                      package = "universalmotif"))

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