recoup (version 1.0.2)

coverageRef: 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, 
        genomeRanges, 
        region = c( "tss", "tes", "genebody", "custom"),
        flank = c(2000, 2000),
        strandedParams = list(strand=NULL, ignoreStrand=TRUE),
        bamParams = NULL,
        rc = NULL
    )

Arguments

input

an input list as in recoup but with the ranges field of each member filled (e.g. after using preprocessRanges).

genomeRanges

the genome from recoup as a GRanges object (e.g. the output from makeGRangesFromDataFrame).

region

see the region argument in the main recoup function.

flank

see the flank argument in the main recoup function.

strandedParams

see the strandedParams argument in the main recoup function.

bamParams

see the bamParams 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.

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, 
    genomeRanges=testGenomeRanges, 
    region="tss",
    flank=c(2000,2000)
)