alleleCounts: Method alleleCounts

In InesdeSantiago/BaalChIP: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Description

Generates allele-specific read count data from each BAM ChIP-seq dataset for each variant.

Usage

alleleCounts(.Object, min_base_quality = 10, min_mapq = 15, verbose = TRUE)

## S4 method for signature 'BaalChIP'
alleleCounts(.Object, min_base_quality = 10, min_mapq = 15, verbose = TRUE)

Arguments

.Object	An object of the BaalChIP class.
min_base_quality	A numeric value indicating the minimum read base quality below which the base is ignored when summarizing pileup information (default 10).
min_mapq	A numeric value indicating the minimum mapping quality (MAPQ) below which the entire read is ignored (default 15).
verbose	logical. If TRUE reports extra information on the process

Details

Utilizes the information within the samples slot of a BaalChIP object. Will primarily find all variants overlapping peaks. Then, for each variant, computes the number of reads carrying the reference (REF) and alternative (ALT) alleles.

Value

An updated BaalChIP object with the slot alleleCounts containing a list of GRanges objects.

Note

BaalChIP computes allelic counts at each variant position with Rsamtools pileup function. The algorithm follows pileup::Rsamtools by automatically excluding reads flagged as unmapped, secondary, duplicate, or not passing quality controls.

Author(s)

Ines de Santiago

See Also

BaalChIP.get

Examples

samplesheet <- system.file("test", "exampleChIP.tsv", package = "BaalChIP")  
hets <- c("MCF7"= system.file("test", "MCF7_hetSNP.txt", package = "BaalChIP"), 
         "GM12891"= system.file("test", "GM12891_hetSNP.txt", package = "BaalChIP"))
res <- BaalChIP(samplesheet=samplesheet, hets=hets)
res <- alleleCounts(res, min_base_quality=10, min_mapq=15)

#retrieve alleleCounts:
counts <- BaalChIP.get(res, 'alleleCountsPerBam')

#alleleCounts are grouped by bam_name and group_name:
names(counts)
names(counts[['MCF7']])

#check out the result for one of the bam files:
counts[['MCF7']][[1]]

InesdeSantiago/BaalChIP documentation built on March 4, 2021, 12:54 a.m.