read_homer: Import HOMER motifs.

In bjmt/universalmotif: Import, Modify, and Export Motifs with R

Import HOMER motifs.

Description

Import HOMER formatted motifs. See http://homer.ucsd.edu/homer/motif/. Assumed to be DNA motifs. Note that HOMER motifs come with a pre-determined logodds threshold; if you wish to re-create HOMER's motif scanning, then use it in scan_sequences() (see examples).

Usage

read_homer(file, skip = 0)

Arguments

file	character(1) File name.
skip	numeric(1) If not zero, will skip however many desired lines in the file before starting to read.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

References

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010). “Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.” Molecular Cell, 38, 576-589.

See Also

Other read_motifs: read_cisbp(), read_jaspar(), read_matrix(), read_meme(), read_motifs(), read_transfac(), read_uniprobe()

Examples

data(ArabidopsisPromoters)
homer <- read_homer(system.file("extdata", "homer.txt",
                                package = "universalmotif"))
thresholds <- homer |> to_df() |> with(logodds.threshold) |> as.numeric()
scan_sequences(homer, ArabidopsisPromoters,
  threshold = thresholds, threshold.type = "logodds.abs")

bjmt/universalmotif documentation built on Nov. 16, 2024, 7:38 a.m.