read_matrix: Import motifs from raw matrices.

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

Import motifs from raw matrices.

Description

Import simply formatted motifs.

Usage

read_matrix(file, skip = 0, type, positions = "columns",
  alphabet = "DNA", sep = "", headers = TRUE, rownames = FALSE,
  comment = NULL)

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.
type	character(1) One of c('PCM', 'PPM', 'PWM', 'ICM'). If missing will try and guess which one.
positions	character(1) One of c('columns', 'rows'). Partial matching allowed. Indicate whether each position within a motif is represented as a row or a column in the file.
alphabet	character(1) One of c('DNA', 'RNA', 'AA'), or a string of letters.
sep	character(1) Indicates how individual motifs are separated. Set as NULL if there are no seperating lines between motifs (the default is to assume a blank line).
headers	logical(1), character(1) Indicating if and how to read names.
rownames	logical(1) Are there alphabet letters present as rownames?
comment	NULL, character(1) Character denoting lines to be considered comments.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

See Also

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

Examples

   hocomoco <- system.file("extdata", "hocomoco.txt", package = "universalmotif")
   hocomoco <- read_matrix(hocomoco, headers = ">", positions = "rows")

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