cnvGetCounts: Count molecules from a bam file overlapping given intervals

In daynefiler/mcCNV: Call copy number variants from whole exome/whole genome sequencing data

Description

cnvGetCounts takes a bam file and an interval object and returns the number of overlapping molecules for each of the given intervals

Usage

cnvGetCounts(bamfile, interval, subject = NULL, verbose = TRUE)

Arguments

bamfile	Character of length 1, the file path to the .bam file
interval	data.table object containing the intervals to count molecules over; see ?cnvValidInterval
subject	Character of length 1, the subject name for bam file; defaults to 'bamfile' parameter when NULL
verbose	TRUE/FALSE

Value

data.table counts object

daynefiler/mcCNV documentation built on Dec. 15, 2021, 3:58 a.m.