read_cisbp: Import CIS-BP motifs.

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

Import CIS-BP motifs.

Description

Import CIS-BP formatted motifs. See http://cisbp.ccbr.utoronto.ca/index.php. Assumed to be DNA motifs.

Usage

read_cisbp(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

CIS-BP motifs can be formatted with or without additional header metadata. Motifs without any header start at instances of the word "Pos", whereas motifs with a header start at instances of the word "TF".

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

References

Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR (2014). “Determination and inference of eukaryotic transcription factor sequence specificity.” Cell, 158, 1431-1443.

See Also

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

Examples

cisbp <- read_cisbp(system.file("extdata", "cisbp.txt",
                                package = "universalmotif"))

bjmt/universalmotif documentation built on March 18, 2024, 8:32 a.m.