GRcoverage-methods: based on a GRanges and a BAM file, returns the total coverage...
In kamalfartiyal84/compEpiTools: Tools for computational epigenomics

Description Methods Examples

GRcoverage returns the total coverage for each range in GRanges, while GRcoverageInbins divides each range in equally-sized bins and returns the total coverage for each bin.

To be used in this form:

GRcoverage(Object, bam, Nnorm=TRUE, Snorm=TRUE)

GRcoverageInbins(Object, bam, Nnorm=TRUE, Snorm=TRUE, Nbins)

where:

Object: GRanges
bam: character; a path to a BAM file
Nnorm: logical; whether to perform library size normalization
Snorm: logical; whether to perform normalization based on the region width in bp
Nbins: numeric; the number of equally sized bins each range in Object is divide into

For each range in the GRanges (or for each bin within the range), the sum of the base coverage in the range is determined.

If Nnorm is TRUE, the coverage is divided by the number of aligned reads in the BAM file, and multiplied by 1e6.

If Snorm is TRUE, the coverage is divided by the region width in bp.

GRcoverage returns an array of region coverages with length equal to the length of the Object GRanges.

GRcoverageInbins returns a matrix with nrow equal to the length of the Object GRanges and ncol equal to Nbins; if Nbins is equal to 1 a matrix of 1 column is returned.

An increasing number of bins, does not correspond to a significant increase in the computation time (65sec for 43k regions and 10 bins).

GRcoverageInbins with Nbins equal to 1 returns counts identical to GRcoverage but it is slightly slower (64sec vs 46sec for 43k regions).

GRcoverageInbins will return NAs and a warning for the rows corresponding to those ranges whose width is lower than the number of bins.

The coverage for sequences not available in the BAM file is set to 0.

The BAM file has to be associated to the corresponding index .bai file. Please refer to the documentation of samtools on how to create it.

bampath <- system.file("extdata", "ex1.bam", package="Rsamtools")
gr <- GRanges(seqnames= Rle(c('seq1','seq2')), 
	ranges=IRanges(start=c(1000, 100), end=c(2000, 1000)))
GRcoverage(Object=gr, bam=bampath, Nnorm=TRUE, Snorm=TRUE)
GRcoverageInbins(Object=gr, bam=bampath, Nnorm=TRUE, Snorm=TRUE, Nbins=4)