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

### See Also

`preprocessIntervals correctCoverageBias runAbsoluteCN`

### 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 2.0.2 Index]