recoup (version 1.0.2)

profileMatrix: 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.

Examples

# Load some data
data("recoup_test_data",package="recoup")
# Do some work
testGenomeRanges <- makeGRangesFromDataFrame(df=test.genome,
    keep.extra.columns=TRUE)
test.input <- coverageRef(
    test.input, 
    genomeRanges=testGenomeRanges, 
    region="tss",
    flank=c(2000,2000)
)
test.input <- profileMatrix(
    test.input,
    flank=c(2000,2000),
    binParams=list(flankBinSize=50,regionBinSize=150,
        sumStat="mean",smooth=TRUE),
    rc=0.5
)