getCountsByID: get counts for large single cell data

In caleblareau/chromVARxx: Augmented functionality for analysis of epigenomic variance

Description

If bulk, use the standard getCounts function in chromVAR. Otherwise, if you have a barcoded sample and a particular sam tag that distinguishes cells, this function should be much faster. Assumes that duplicate reads are already removed and other artifacts (e.g. proper pairing) are also already handled upstream.

Usage

getCountsByID(bamfile, peaks, barcodeTag, mapqFilter)

## S4 method for signature 'character,GenomicRanges,character,numeric'
getCountsByID(bamfile,
  peaks, barcodeTag, mapqFilter = 0)

Arguments

bamfile	Valid string for filepath to bam file
peaks	A GRanges object of accessibility peaks. Use chromVAR::getPeaks to import a bed file for this.
barcodeTag	The two-letter sam tag associated with the barcoding of the different cells
mapqFilter	Minimum mapping quality metric necessary for read to be used in counts matrix.

Value

A summarized Experiment roughly equivalent to what chromVAR::getCoutns would provide

Methods (by class)

• bamfile = character,peaks = GenomicRanges,barcodeTag = character,mapqFilter = numeric:

Author(s)

Caleb Lareau

Examples

bamfile <-paste0(system.file('raw',package='chromVARxx'),'/chr1.barcode.small.bam')
peakfile <- paste0(system.file('raw',package='chromVARxx'),'/chr1.peaks.small.bed')
peaks <- suppressWarnings(chromVAR::getPeaks(peakfile))
barcodeTag <- "CB"
SE <- getCountsByID(bamfile, peaks, barcodeTag, mapqFilter =0 )

caleblareau/chromVARxx documentation built on May 14, 2019, 11:15 a.m.