calculateBamCoverageByInterval {PureCN} | R Documentation |
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.
calculateBamCoverageByInterval(bam.file, interval.file, output.file = NULL, index.file = bam.file, keep.duplicates = FALSE, ...)
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 |
index.file |
The bai index. This is expected without the .bai file
suffix, see |
keep.duplicates |
Keep or remove duplicated reads. |
... |
Additional parameters passed to |
Returns total and average coverage by intervals.
Markus Riester
preprocessIntervals
correctCoverageBias runAbsoluteCN
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)