Read motifs from a HOMER motif format file

Source: R/motif-import.R

Parses a HOMER .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_homer(file)

Arguments

file

character(1) path to a HOMER motif file (.motif).

Value

A named list of numeric matrices. Each matrix has columns A, C, G, T and one row per motif position. List names are derived from the consensus sequence. Each matrix carries the following attributes:

name

Motif name / description from the header

consensus

Consensus sequence from the header

log_odds_threshold

Detection threshold (numeric)

log_p_value

Log p-value (numeric)

w

Motif width (integer)

source

"homer"

See also

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

Examples

if (FALSE) { # \dontrun{
motifs <- gseq.read_homer("known_motifs.motif")
names(motifs)
m <- motifs[[1]]
head(m)
attr(m, "consensus")
} # }