motifSummarization: Map Peaks to DNA motifs in scATAC-seq Data

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

Map Peaks to DNA motifs in scATAC-seq Data

Description

Provides functionality to summarize scATAC-seq data by motifs from peak summary. Uses motifmatchr to prepare data for CoGAPS run using motif summarization

Usage

motifSummarization(
  motifList,
  scATACData,
  granges,
  genome,
  cellNames,
  pCutoff = 5e-09
)

Arguments

motifList	PWMatrixList object of motifs (from the TFBS tools package)
scATACData	matrix of scATACseq data, peaks (rows) by cells (columns)
granges	GenomicRanges object corresponding to all peaks used to summarize scATACData
genome	The UCSC Genome to use for input to motifmatchr (e.g "hg19")
cellNames	List of cellnames corresponding to the cells in scATACData
pCutoff	p-value cutoff for motifmatchr, 5e-09 by default to identify only matches with high confidence

Value

matrix for input to CoGAPS with summary to motifs; motifs by cells

Examples

## Not run: 
motifSummTest = motifSummarization(motifList = motifs, scATACData = scatac,
 granges = peakGranges, genome = "hg19", cellNames = cells, pCutoff = 5e-09)

## End(Not run)

FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.