coverageRnaRef {recoup}R Documentation

Calculate coverage in a set of reference genomic regions (RNA-Seq or spliced mode)

Description

This function fills the coverage field in the main input argument in recoup function.

Usage

    coverageRnaRef(
        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

a named GRangesList where list member names are genes and list members are GRanges representing each gene's exons.

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")

# Note: the figures that will be produced will not look 
# realistic or pretty and will be "bumpy". This is because 
# package size limitations posed by Bioconductor guidelines 
# do not allow for a full test dataset. As a result, the input
# below is not an RNA-Seq dataset. Have a look at the
# vignette on how to test with more realistic data.

# Calculate coverages
testGenomeRanges <- makeGRangesFromDataFrame(df=test.genome,
    keep.extra.columns=TRUE)
test.input <- coverageRnaRef(
    test.input,
    mainRanges=test.exons
)
[Package recoup version 1.10.1 Index]