misha (version 5.11.23)

gseq.read_meme: Read motifs from a MEME minimal motif format file

Description

Parses a MEME minimal motif format file and returns a named list of position probability matrices (PPM). Each matrix has rows corresponding to motif positions and columns A, C, G, T. The returned matrices are directly usable with gseq.pwm.

Usage

gseq.read_meme(file)

Value

A named list of numeric matrices. Each matrix has columns

A, C, G, T and one row per motif position. List names are motif identifiers. Each matrix carries the following attributes:

name

Motif name / alternate ID (second token on the MOTIF line)

alength

Alphabet length (integer, typically 4)

w

Motif width (integer, number of positions)

nsites

Number of sites used to build the matrix (numeric; NA if absent)

E

E-value (numeric; NA if absent)

url

URL string if present, otherwise NA

strand

Strand specification from the file header (e.g. "+ -")

background

Named numeric vector of background frequencies (c(A=..., C=..., G=..., T=...)), or NULL if absent

Arguments

file

character(1) path to a MEME format file (.meme, .txt).

See Also

Other motif functions: gseq.read_homer(), gseq.read_jaspar()

Examples

if (FALSE) {
motifs <- gseq.read_meme("JASPAR2024_CORE_vertebrates.meme")
names(motifs)
m <- motifs[[1]]
head(m)
attr(m, "name")
attr(m, "nsites")
}