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

In misha: Toolkit for Analysis of Genomic Data

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)

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

## Not run: 
motifs <- gseq.read_meme("JASPAR2024_CORE_vertebrates.meme")
names(motifs)
m <- motifs[[1]]
head(m)
attr(m, "name")
attr(m, "nsites")

## End(Not run)

misha documentation built on Aug. 24, 2026, 5:14 p.m.