read_jaspar: Import JASPAR motifs.

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

Import JASPAR motifs.

Description

Import JASPAR formatted motifs. See http://jaspar.genereg.net/. Can be either DNA, RNA, or AA motifs.

Usage

read_jaspar(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.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

References

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Cheneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A (2018). “JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.” Nucleic Acids Research, 46, D260-D266.

See Also

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

Examples

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

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