SNPs enrichment

[lukais-iohan]

Hi,

I have a list of SNPs from a GWAS performed on a group of Alzheimer's patients. Does it possible to see if these SNPs are enriched in chromatin accesible regions with ArchR?

[rcorces]

We dont provide anything specifically to do this. We do have a new function on the dev branch to do hypergeometric enrichment but I think you might be better suited by something else.

ArchR/R/AnnotationPeaks.R

Lines 1053 to 1060 in 3c65039

	#' 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.

[lukais-iohan]

Thanks for your quick answer. I will try your suggestion.

Bests