getCoverage: Import coverage data from .bam file

In gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines

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)

gmoviz documentation built on Nov. 8, 2020, 5:41 p.m.