coverageRnaRef: Calculate coverage in a set of reference genomic regions...
In recoup: An R package for the creation of complex genomic profile plots

Description Usage Arguments Value Author(s) Examples

*This function is defunct! Please use coverageRef.* This function fills the coverage field in the main input argument in recoup function.

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    coverageRnaRef( input, mainRanges,
        strandedParams = list(strand=NULL, ignoreStrand=TRUE),
        rc = NULL)

`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).

Same as input with the ranges fields filled.

Panagiotis Moulos

# 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 <- coverageRef(
#    test.input,
#    mainRanges=test.exons
#)