write_homer {universalmotif}R Documentation

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 = 0.6, overwrite = FALSE,
  append = FALSE)

Arguments

motifs

See convert_motifs() for acceptable formats.

file

character(1) File name.

logodds_threshold

numeric Stringency required for HOMER to match a motif. See scan_sequences().

overwrite

logical(1) Overwrite existing file.

append

logical(1) Add to an existing file.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

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(4), 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())


[Package universalmotif version 1.8.5 Index]