calcCoverage: Calculate coverages over a genomic region
In recoup: An R package for the creation of complex genomic profile plots

Description Usage Arguments Details Value Author(s) Examples

This function returns a coverage list for the genomic regions in mask argument. Generally it should not be used alone and is intended for internal use, although it is useful for calculating stand-alone coverages.

1 2	calcCoverage(input, mask, strand = NULL, ignore.strand = TRUE, rc = NULL)

`input`	a `GRanges` object or a list of `GRanges` (not a `GRangesList`!) or the path to a BAM or BigWig file.
`mask`	a `GRanges` or `GRangesList` object.
`strand`	see the `strandedParams` in the main `recoup` function.
`ignore.strand`	see the `strandedParams` in the main `recoup` function.
`rc`	fraction (0-1) of cores to use in a multicore system. It defaults to `NULL` (no parallelization).

input contains the short reads in one of the formats described in the arguments section. When input is a list, this list should contain one member per chromosome of the organism of interest.

mask contains the genomic regions over which the coverage will be calculated from the input reads. When calculating RNA-Seq profiles, mask must be a named GRangesList where each member represents the exons of the respective gene.

A list of Rle objects representing the genomic coverages of interest.

Panagiotis Moulos

# Load some data
data("recoup_test_data",package="recoup")

# Calculate coverage Rle
mask <- makeGRangesFromDataFrame(df=test.genome,
    keep.extra.columns=TRUE)
small.cov <- calcCoverage(test.input[[1]]$ranges,mask)