R: Function to calculate coverage from BAM file

calculateBamCoverageByInterval {PureCN}

R Documentation

Function to calculate coverage from BAM file

Description

Takes a BAM file and an interval file as input and returns coverage for each interval. Coverage should be then GC-normalized using the correctCoverageBias function before determining purity and ploidy with runAbsoluteCN. Uses the scanBam function and applies low quality, duplicate reads as well as secondary alignment filters.

Usage

calculateBamCoverageByInterval(bam.file, interval.file, output.file = NULL,
  index.file = bam.file, keep.duplicates = FALSE, ...)

Arguments

`bam.file`	Filename of a BAM file.
`interval.file`	File specifying the intervals. Interval is expected in first column in format CHR:START-END.
`output.file`	Optionally, write minimal coverage file. Can be read with the `readCoverageFile` function.
`index.file`	The bai index. This is expected without the .bai file suffix, see `?scanBam`.
`keep.duplicates`	Keep or remove duplicated reads.
`...`	Additional parameters passed to `ScanBamParam`.

Value

Returns total and average coverage by intervals.

Author(s)

Markus Riester

Examples


bam.file <- system.file("extdata", "ex1.bam", package = "PureCN",
    mustWork = TRUE)
interval.file <- system.file("extdata", "ex1_intervals.txt",
    package = "PureCN", mustWork = TRUE)

# Calculate raw coverage from BAM file. These need to be corrected for
# GC-bias using the correctCoverageBias function before determining purity
# and ploidy.
coverage <- calculateBamCoverageByInterval(bam.file = bam.file,
    interval.file = interval.file)

[Package PureCN version 1.12.2 Index]