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,
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, benjamin.tremblay@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 1.11.17
Index]