calcCoverage {recoup} | R Documentation

## Calculate coverages over a genomic region

### Description

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.

### Usage

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

### Arguments

`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).

### Details

`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.

### Value

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

### Author(s)

Panagiotis Moulos

### Examples

    # 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)

[Package recoup version 1.10.1 Index]