profileMatrix {recoup} | R Documentation

## Calculate final profile matrices for plotting

### Description

This function fills the `profile` field in the main `input` argument in `recoup` function by calculating profile matrices from coverages which will be used for plotting.

### Usage

        profileMatrix(input, flank, binParams, rc = NULL)

### Arguments

`input` | an input list as in `recoup` but with the `ranges` the `coverage` fields of each member filled (e.g. after using `preprocessRanges` and `coverageRef`).
`flank` | see the `flank` argument in the main `recoup` function.
`binParams` | see the `binParams` 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 `profile` fields filled.

### Author(s)

Panagiotis Moulos

### Examples

    # Load some data
    data("recoup_test_data",package="recoup")
    # Do some work
    testGenomeRanges <- makeGRangesFromDataFrame(df=test.genome,
        keep.extra.columns=TRUE)
    w <- width(testGenomeRanges)
    testGenomeRanges <- promoters(testGenomeRanges,upstream=2000,downstream=0)
    testGenomeRanges <- resize(testGenomeRanges,width=w+4000)
    test.input <- coverageRef(
        test.input,
        mainRanges=testGenomeRanges
    )
    test.input <- profileMatrix(
        test.input,
        flank=c(2000,2000),
        binParams=list(flankBinSize=50,regionBinSize=150,
            sumStat="mean",interpolation="auto"),
        rc=0.5
    )

[Package recoup version 1.12.0 Index]