coverageRef {recoup} | R Documentation

## Calculate coverage in a set of reference genomic regions (ChIP-Seq or unspliced mode)

### Description

This function fills the `coverage` field in the main `input` argument in `recoup` function.

### Usage

        coverageRef(
            input,
            mainRanges,
            strandedParams = list(strand=NULL, ignoreStrand=TRUE),
            rc = NULL
        )

### Arguments

`input` | an input list as in `recoup` but with the `ranges` field of each member filled (e.g. after using `preprocessRanges`).
`mainRanges` | the `genome` from `recoup` as a `GRanges` object (e.g. the output from `makeGRangesFromDataFrame`).
`strandedParams` | see the `strandedParams` argument in the main `recoup` function.
`rc` | fraction (0-1) of cores to use in a multicore system. It defaults to `NULL` (no parallelization).

### Value

Same as input with the `ranges` fields filled.

### Author(s)

Panagiotis Moulos

### Examples

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

    # Calculate coverages
    testGenomeRanges <- makeGRangesFromDataFrame(df=test.genome,
        keep.extra.columns=TRUE)
    test.input <- coverageRef(
        test.input,
        mainRanges=testGenomeRanges
    )

[Package recoup version 1.8.0 Index]