| read_matrix {universalmotif} | R Documentation |
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)
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').
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.
|
headers |
logical(1), character(1) Indicating if and how to read names.
|
rownames |
logical(1) Are there alphabet letters present as rownames?
|
Value
list universalmotif objects.
Author(s)
Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca
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")
[Package
universalmotif version 1.4.10
Index]