gseq.read_jaspar: Read motifs from a JASPAR PFM format file

In misha: Toolkit for Analysis of Genomic Data

Read motifs from a JASPAR PFM format file

Description

Parses a JASPAR Position Frequency Matrix (PFM) file and returns a named list of position probability matrices (PPM). Supports both the standard JASPAR header format (>ID NAME followed by labeled rows) and the simple 4-row PFM format. Counts are converted to probabilities by dividing each column by its column sum.

Usage

gseq.read_jaspar(file)

Arguments

file	character(1) path to a JASPAR format file (.jaspar, .pfm, .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 from the header line

w

Motif width (integer)

nsites

Total counts per position (numeric; NA for simple-format files)

format

Sub-format detected: "jaspar" or "simple"

See Also

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

Examples

## Not run: 
motifs <- gseq.read_jaspar("JASPAR2024_CORE.jaspar")
names(motifs)
m <- motifs[[1]]
head(m)

## End(Not run)

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