profileMatrix: Calculate final profile matrices for plotting

In pmoulos/recoup: An R package for the creation of complex genomic profile plots

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, 
        .feNoSplit = FALSE)

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).
.feNoSplit	Temporary internal variable. Do not change unless you know what you are doing!

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=0.1
)

pmoulos/recoup documentation built on May 20, 2024, 2:22 a.m.