Motif enrichment in a subset of peaks

[aselewa]

Hi,

I am wondering if theres a way to estimate motif enrichment in any subset of the union peak set? In other words, I am trying to estimate motif enrichment in peaks that are shared across all cell-types. I was able to define the shared peaks using my own way, but I am wondering how I can feed these to peakAnnoEnrichment?

Thanks so much.

[rcorces]

Just change your peakSet using addPeakSet()?

[cristanchoa]

I have a similar question. I am trying to obtain the motif analysis on peaks shared across cell types but still from the same peaks that were initially called. Would you mind sharing how you think you got it to work, @aselewa?

[aselewa]

Hi, I dont access to my code anymore, but I remember formatting my union set to look like the seMarker object and giving that to peakAnnoEnrichment. You can print out the seMarker object from differential accessibility to see what it looks like, but its basically a summerized experiment object. Theres a few columns in the metadata but I left them as null and ArchR didnt complain.

Its pretty hacky so I would check if ArchR devs have made something since then.

[Y-ogativity]

I have a similar question. It would be very convenient for me to use the peakAnnoErichmet function with a custom set of peaks (e.g., shared peaks across cell types) that have already been called.

[trinevd]

Hi. I have a similar problem. I'd like to perform motif enrichment analysis on subset of peaks shared or unique across cell types, and get the same error.

[rcorces]

There is a new function on the dev branch called customEnrichment() which should enable what you are looking for.

ArchR/R/AnnotationPeaks.R

Lines 1053 to 1146 in c44b50c

	#' Hypergeometric Enrichment in input peak ranges.
	#'
	#' This function will perform hypergeometric enrichment of a given peak matches object and ranges.
	#'
	#' @param ranges A `GenomicRanges` object of peaks/regions to overlap with peaks.
	#' @param matches A custom `peakAnnotation` matches object used as input for the hypergeometric test. See
	#' `motifmatchr::matchmotifs()` for additional information.
	#' @param bgdPeaks A `SummarizedExperiment` of background peaks from `getBgdPeaks` can be NULL for using all peaks.
	#'
	#' @examples
	#' #Project
	#' proj <- getTestProject()
	#'
	#' #Get Peaks
	#' peaks <- getPeakSet(proj)
	#'
	#' #Custom C1 Mono
	#' peaks1 <- peaks[names(peaks)=="C1"]
	#'
	#' #All Peaks
	#' customEnrichment(
	#' ranges = peaks1,
	#' matches = getMatches(proj)
	#' )
	#' # feature CompareFrequency nCompare CompareProportion BackgroundFrequency
	#' # CEBPB_1 CEBPB_1 70 635 0.11023622 122
	#' # CEBPA_2 CEBPA_2 81 635 0.12755906 156
	#' # IRF4_4 IRF4_4 103 635 0.16220472 276
	#' # EOMES_6 EOMES_6 36 635 0.05669291 120
	#' # ETS1_3 ETS1_3 38 635 0.05984252 149
	#' # PAX5_5 PAX5_5 23 635 0.03622047 124
	#' # nBackground BackgroundProporition Enrichment mlog10p mlog10Padj
	#' # CEBPB_1 2142 0.05695612 1.9354589 10.3279 9.373657
	#' # CEBPA_2 2142 0.07282913 1.7514839 8.9394 7.985157
	#' # IRF4_4 2142 0.12885154 1.2588497 2.6938 1.739557
	#' # EOMES_6 2142 0.05602241 1.0119685 0.3001 0.000000
	#' # ETS1_3 2142 0.06956116 0.8602864 0.0487 0.000000
	#' # PAX5_5 2142 0.05788982 0.6256795 0.0006 0.000000
	#'
	#' #Background Peaks
	#' customEnrichment(
	#' ranges = peaks1,
	#' matches = getMatches(proj),
	#' bgdPeaks = getBgdPeaks(proj, force=TRUE)
	#' )
	#' # feature CompareFrequency nCompare CompareProportion BackgroundFrequency
	#' # CEBPB_1 CEBPB_1 70 635 0.11023622 2459
	#' # CEBPA_2 CEBPA_2 81 635 0.12755906 3154
	#' # IRF4_4 IRF4_4 103 635 0.16220472 4836
	#' # ETS1_3 ETS1_3 38 635 0.05984252 1781
	#' # EOMES_6 EOMES_6 36 635 0.05669291 1975
	#' # PAX5_5 PAX5_5 23 635 0.03622047 1495
	#' # nBackground BackgroundProporition Enrichment mlog10p mlog10Padj
	#' # CEBPB_1 32385 0.07593021 1.4518097 2.9544 2.000157
	#' # CEBPA_2 32385 0.09739077 1.3097654 2.1341 1.179857
	#' # IRF4_4 32385 0.14932839 1.0862283 0.7142 0.000000
	#' # ETS1_3 32385 0.05499460 1.0881527 0.4975 0.000000
	#' # EOMES_6 32385 0.06098502 0.9296203 0.1551 0.000000
	#' # PAX5_5 32385 0.04616335 0.7846154 0.0422 0.000000
	#' #
	#' @export
	customEnrichment <- function(
	ranges = NULL,
	matches = NULL,
	bgdPeaks = NULL
	){
	if(is.null(matches)){
	stop("Please supply matches! Try `matches` = getMatches(ArchRProj)!")
	}
	.validInput(input = ranges, name = "ranges", valid = c("granges"))
	.validInput(input = matches, name = "matches", valid = c("SummarizedExperiment"))
	.validInput(input = bgdPeaks, name = "bgdPeaks", valid = c("SummarizedExperiment", "null"))
	if(!is.null(bgdPeaks)){
	rownames(matches) <- paste0(rowRanges(matches))
	rownames(bgdPeaks) <- paste0(rowRanges(bgdPeaks))
	bgdPeaks <- bgdPeaks[rownames(matches), ]
	idx <- unique(queryHits(findOverlaps(matches, ranges, ignore.strand=TRUE)))
	.computeEnrichment(matches, idx, c(idx, as.vector(assay(bgdPeaks)[idx,])))
	}else{
	idx <- unique(queryHits(findOverlaps(matches, ranges, ignore.strand=TRUE)))
	.computeEnrichment(matches, idx, seq_len(nrow(matches)))
	}
	}