predictGenePeakPair: Link Distal Regulatory Elements (peaks) to Putative Target...

In r3fang/SnapATAC: Single Nucleus Analysis Package for ATAC-Seq

Link Distal Regulatory Elements (peaks) to Putative Target Genes

Description

Link Distal Regulatory Elements (peaks) to Putative Target Genes

Usage

predictGenePeakPair(obj, input.mat = c("pmat", "bmat"), gene.name = NULL,
  gene.loci = NULL, do.par = FALSE, num.cores = 1)

Arguments

obj	A snap object.
input.mat	Input matrix c("pmat", "bmat").
gene.name	Name of the target gene. It must be a gene in the cell-by-gene matrix [NULL].
gene.loci	A genomic range object that contains the flanking window of the target gene [NULL].
do.par	A logical variable indicates if to run this in parallel using multiple processors [FALSE].
num.cores	A numeric class that indicates the number of cores to use for calculation [1].

Value

Return A data.frame that contains the peaks and associating P-value.

r3fang/SnapATAC documentation built on March 29, 2022, 4:33 p.m.