getCellAlleleCount: Get alternative allele count for positions of interest for...

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Get alternative allele count for positions of interest for multiple cells from one bam

Usage

getCellAlleleCount(gr, bamFile, indexFile, cellBarcodes, verbose = FALSE,
  n.cores = 1)

Arguments

gr	GenomicRanges object for positions of interest
bamFile	bam file containing all cells indexed by barcode (such as 10X)
indexFile	bai index file
cellBarcodes	vector of valid cell barcodes annotated as CB in the bam
verbose	Boolean of whether or not to print progress and info
n.cores	Number of cores; Can parallelize across cells

Value

refCount reference allele count information for each position of interest altCount alternative allele count information for each position of interest

Examples

## Not run: 
## Get putative hets from ExAC
load(system.file("ExAC", "ExAC_chr1.RData", package = "HoneyBADGER"))
head(snps)
cov <- getCoverage(snps, bamFile, indexFile, verbose=TRUE)
## for the sites with coverage, get all cells
vi <- cov>0
snps.cov <- snps[vi,]
barcodes <- c('AAACATACAAAACG-1', 'AAACATACAAAAGC-1', 'AAACATACAAACAG-1')
mats.chr1 <- getCellAlleleCount(snps.cov, bamFile, indexFile, barcodes, verbose=TRUE, n.cores=10)

## End(Not run)

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.