coverageRef: Calculate coverage in a set of reference genomic regions...

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

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
)

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