write_homer: Export motifs in HOMER format.

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

Export motifs in HOMER format.

Description

Convert DNA motifs to HOMER format and write to file. See http://homer.ucsd.edu/homer/motif/.

Usage

write_homer(motifs, file, logodds_threshold = NULL, overwrite = FALSE,
  append = FALSE, threshold = 0.8, threshold.type = c("logodds",
  "logodds.abs", "pvalue"))

Arguments

motifs	See convert_motifs() for acceptable formats.
file	character(1) File name.
logodds_threshold	Deprecated. If set, read_homer() will behave like pre-version 1.12.0 of the universalmotif package for backwards compatibility (though a warning will be printed).
overwrite	logical(1) Overwrite existing file.
append	logical(1) Add to an existing file.
threshold	numeric(1) Stringency required for HOMER to match a motif. See scan_sequences() for how to use this argument. Can be a single value to be recycled for all motifs, or a vector of equal length to the number of motifs.
threshold.type	character(1) How the threshold value should be used to obtain the final threshold value in the written motif. See scan_sequences() for how to use this.

Value

NULL, invisibly.

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

read_homer()

Other write_motifs: write_jaspar(), write_matrix(), write_meme(), write_motifs(), write_transfac()

Examples

motif <- create_motif()
write_homer(motif, tempfile())

bjmt/universalmotif documentation built on March 18, 2024, 8:32 a.m.