motifPeakZtest: Peak-based TF motif enrichment Z-test

In buenrostrolab/FigR: Functional Inference of Gene Regulation (FigR) using paired single cell ATAC-seq and RNA-seq data

Peak-based TF motif enrichment Z-test

Description

Wrapper function to assess a specific set of peaks for enrichment with respect to TF binding motifs using a Z test after adjusting for GC bias and Tn5 accessibility

Usage

motifPeakZtest(peakSet, bgPeaks, tfMat)

Arguments

peakSet	vector of peak indices you wish to test for motif enrichment
bgPeaks	background peaks matrix returned by getBackgroundPeaks function in chromVAR
tfMat	binary match sparseMatrix object of (reference) peaks by TF motifs returned by matchMotifs function

Value

data frame of motif enrichment results rank sorted by significance and frequency of motifs in the peakset, respectively

Author(s)

Vinay Kartha, Samuel Rose, and Jason D. Buenrostro

buenrostrolab/FigR documentation built on Feb. 10, 2023, 11:26 a.m.