merge_motifs: Merge motifs.

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

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. Motifs are merged one at a time, starting with the first entry in the list.

Usage

merge_motifs(motifs, method = "ALLR", use.type = "PPM", min.overlap = 6,
  min.mean.ic = 0.25, tryRC = TRUE, relative_entropy = FALSE,
  normalise.scores = FALSE, min.position.ic = 0, score.strat = "sum",
  new.name = NULL)

Arguments

motifs	See convert_motifs() for acceptable motif formats.
method	character(1) One of PCC, EUCL, SW, KL, ALLR, BHAT, HELL, SEUCL, MAN, ALLR_LL, WEUCL, WPCC. 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. Note that 'ICM' is not allowed when method = c("ALLR", "ALLR_LL").
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 between 0 and 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. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use average_ic() to filter out low IC motifs to get around this if you want to avoid getting NAs in your output.
tryRC	logical(1) Try the reverse complement of the motifs as well, report the best score.
relative_entropy	logical(1) Change the ICM calculation affecting min.position.ic and min.mean.ic. 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.
min.position.ic	numeric(1) Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with normalise.scores = TRUE, as this will help punish scores resulting from only a fraction of an alignment.
score.strat	character(1) How to handle column scores calculated from motif alignments. "sum": add up all scores. "a.mean": take the arithmetic mean. "g.mean": take the geometric mean. "median": take the median. "wa.mean", "wg.mean": weighted arithmetic/geometric mean. "fzt": Fisher Z-transform. Weights are the total information content shared between aligned columns.
new.name	character(1), NULL Instead of collapsing existing names (if NULL), assign a new one manually for the merged motif.

Details

See compare_motifs() for more info on comparison parameters.

If using a comparison metric where 0s are not allowed (KL, ALLR, ALLR_LL, IS), then pseudocounts will be added internally. These pseudocounts are only used for comparison and alignment, and are not used in the final merging step.

Note: score.strat = "a.mean" is NOT recommended, as merge_motifs() will not discriminate between two alignments with equal mean scores, even if one alignment is longer than the other.

Value

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

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

See Also

compare_motifs()

Examples

## Not run: 
library(MotifDb)
merged.motif <- merge_motifs(MotifDb[1:5])

## End(Not run)

m1 <- create_motif("TTAAACCCC", name = "1")
m2 <- create_motif("AACC", name = "2")
m3 <- create_motif("AACCCCGG", name = "3")
view_motifs(merge_motifs(c(m1, m2, m3)))

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