read_jaspar {universalmotif}R Documentation

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, b2tremblay@uwaterloo.ca

References

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon J, van der Lee R, Bessy A, Cheneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas D, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman W, 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"))


[Package universalmotif version 1.2.0 Index]