coverageRnaRef: 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 (RNA-Seq or spliced mode)

Description

*This function is defunct! Please use coverageRef.* 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 <- coverageRef(
#    test.input,
#    mainRanges=test.exons
#)

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