Read motifs from a MEME minimal motif format file

Source: R/motif-import.R

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.

gseq.read_meme(file)

Arguments

file

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

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

See also

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

Examples

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