write_matrix: Export motifs as raw matrices.

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

Export motifs as raw matrices.

Description

Write motifs as simple matrices with optional headers to file.

Usage

write_matrix(motifs, file, positions = "columns", rownames = FALSE, type,
  sep = "", headers = TRUE, overwrite = FALSE, append = FALSE,
  digits = 6)

Arguments

motifs	See convert_motifs() for acceptable formats.
file	character(1) File name.
positions	character(1) One of c('columns', 'rows'). Partial matching allowed.
rownames	logical(1) Include alphabet letters as rownames.
type	character(1) One of c('PCM', 'PPM', 'PWM', 'ICM'). If missing will use whatever type the motif is currently stored as.
sep	character(1) Indicates how to separate individual motifs. Set as NULL to have no seperating lines between motifs (the default is to use a blank line).
headers	logical(1), character(1) Indicating if and how to write names.
overwrite	logical(1) Overwrite existing file.
append	logical(1) Add to an existing file.
digits	numeric(1) Number of digits to use for motif positions.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

See Also

read_matrix()

Other write_motifs: write_homer(), write_jaspar(), write_meme(), write_motifs(), write_transfac()

Examples

motif <- create_motif()
write_matrix(motif, tempfile(), headers = ">")

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