runChromVAR: Estimate Motif Variability Using ChromVAR

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

Estimate Motif Variability Using ChromVAR

Description

Estimate Motif Variability Using ChromVAR

Usage

runChromVAR(obj, input.mat = c("pmat", "bmat"),
  genome = BSgenome.Hsapiens.UCSC.hg19, min.count = 10,
  species = "Homo sapiens")

Arguments

obj	A snap object.
input.mat	Input matrix used for chromVAR analysis c("pmat", "bmat").
genome	BSgenome object that contains the sequence for the corresponding genome (i.e. BSgenome.Hsapiens.UCSC.hg19).
min.count	Min count for features. Features of count lower than min.count will be filtered [10].
species	Species or jaspar code used by 'getJasparMotifs'to get the motif database ["Homo sapiens"].

Value

Return a matrix object that contains the cell-by-motif matrix

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