Import TRANSFAC formatted motifs. Assumed to be DNA motifs, type PCM.
system.file("extdata", "transfac.txt", pacakge="universalmotif")
for an example motif.
read_transfac(file, skip = 0)
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.
list universalmotif objects.
Benjamin Jean-Marie Tremblay, firstname.lastname@example.org
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.
transfac <- read_transfac(system.file("extdata", "transfac.txt", package = "universalmotif"))
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