Increase pvalue cutoff for motifmatchr when running AddMotifs?

[owenwilkins]

Is there a way to increase the p.cutoff argument of motifmatchr::matchMotifs() when using AddMotifs() in signac.

The default value of 5e-5 is quite low and I expect generates quite a lot of false positives, causing the number of enriched motifs to be inflated when running FindMotifs.

[timoast]

You can create the Motif object yourself using the CreateMotifObject() function, this will allow you to run the matchMotifs() function yourself (or any other function to create the motif position matrix). See this code for example:

signac/R/motifs.R

Lines 32 to 59 in 2ad6c3c

	motif.matrix <- CreateMotifMatrix(
	features = object,
	pwm = pfm,
	genome = genome,
	use.counts = FALSE
	)
	if (verbose) {
	message("Finding motif positions")
	}
	# for positions, a list of granges is returned
	# each element of list is a PFM name
	# each entry in granges is the position within a feature that matches motif
	obj_keep <- as.character(seqnames(x = object)) %in% seqlevels(x = genome)
	motif.positions <- motifmatchr::matchMotifs(
	pwms = pfm,
	subject = object[obj_keep],
	out = 'positions',
	genome = genome
	)
	if (verbose) {
	message("Creating Motif object")
	}
	motif <- CreateMotifObject(
	data = motif.matrix,
	positions = motif.positions,
	pwm = pfm
	)

[owenwilkins]

fantastic, thanks