getCoverage {gmoviz} | R Documentation

## Import coverage data from .bam file

### Description

Uses RSamtools to import coverage data from .bam file and format it appropriately for plotting with gmoviz.

### Usage

    getCoverage(regions_of_interest, bam_file, window_size = 1,
      smoothing_window_size = NULL)

### Arguments

`regions_of_interest` | either a GRanges of regions OR a character vector of sequences/chromosomes to find the coverage for (please be careful that the names here match the spelling/format of those in the bam file).
`bam_file` | Location of the bam file from which to read coverage data.
`window_size` | The size of the window to for calculating coverage (default is 1; per base coverage). Use `smoothCoverage` to smooth the data, this is more for reducing time taken to read in and plot coverage over a large number of bases.
`smoothing_window_size` | If supplied, then moving average smoothing will be applied using the `movavg` function from the package pracma (please make sure it's installed). Note: smoothing may take some time when there are many points involved. Please be patient, or proceed without smoothing.

### Value

A GRanges containing the coverage data in the metadata column 'coverage'.

### See Also

The `gmovizInitialise`, `drawLinegraphTrack`, `insertionDiagram` and `featureDiagram` functions which can plot the coverage data.

### Examples

    ## the example .bam file
    path <- system.file('extdata', 'ex1.bam', package='Rsamtools')

    ## example without smoothing or windowing
    getCoverage(regions_of_interest='seq1', bam_file=path)

    ## using windowing
    getCoverage(regions_of_interest='seq1', bam_file=path, window_size=5)

    ## using smoothing
    getCoverage(regions_of_interest='seq1', bam_file=path,
    smoothing_window_size=3)

    ## specifying only a particular region to read in using GRanges
    small_range <- GRanges('seq1', IRanges(0, 500))
    getCoverage(regions_of_interest=small_range, bam_file=path)
    ## please be very careful that the sequence names are spelled exactly like
    ## in the bam file or you'll get an error! The following WON'T WORK.
    ## Not run:
    getCoverage(regions_of_interest='chr1', bam_file=path)
    ## End(Not run)

[Package gmoviz version 1.0.1 Index]