merge_motifs {universalmotif}R Documentation

Merge motifs.

Description

Aligns the motifs using compare_motifs(), then averages the motif PPMs. Currently the multifreq slot, if filled in any of the motifs, will be dropped.

Usage

merge_motifs(motifs, method = "MPCC", use.type = "PPM",
  min.overlap = 6, min.mean.ic = 0.5, tryRC = TRUE,
  relative_entropy = FALSE, normalise.scores = FALSE)

Arguments

motifs

See convert_motifs() for acceptable motif formats.

method

character(1) One of c('PCC', 'MPCC', 'EUCL', 'MEUCL', 'SW', 'MSW', 'KL', 'MKL'). See details.

use.type

character(1) One of 'PPM' and 'ICM'. The latter allows for taking into account the background frequencies if relative_entropy = TRUE.

min.overlap

numeric(1) Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number less than 1, representing the minimum fraction that the motifs must overlap.

min.mean.ic

numeric(1) Minimum mean information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs.

tryRC

logical Try the reverse complement of the motifs as well, report the best score.

relative_entropy

logical(1) For ICM calculation. See convert_type().

normalise.scores

logical(1) Favour alignments which leave fewer unaligned positions, as well as alignments between motifs of similar length. Similarity scores are multiplied by the ratio of aligned positions to the total number of positions in the larger motif, and the inverse for distance scores.

Value

A single motif object. See convert_motifs() for available formats.

Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

See Also

compare_motifs()

Examples

if (requireNamespace("MotifDb", quietly = TRUE) && .Platform$OS.type == "unix") {
  library(MotifDb)
  merged.motif <- merge_motifs(MotifDb[1:5])
}


[Package universalmotif version 1.0.22 Index]