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. Only 0-order background probabilities will be kept.
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 1.2.0
Index]