recoup (version 1.0.2)

preprocessRanges: Read and preprocess BAM/BED files to GRanges

Description

This function reads the BAM/BED files present in the input list object and fills the ranges field of the latter. At the same time it takes care of certain preprocessing steps like normalization.

Usage

preprocessRanges(input, preprocessParams, 
        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).

preprocessParams

see the preprocessParams 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

• This function fills the ranges field in the main input argument in recoup function.

Examples

# This example only demonstrates the usage of the
    # preprocessRanges function. The input BAM files
    # included with the package will not produce
    # realistic plots as they contain only a very small
    # subset of the original data presented in the 
    # vignettes (50k reads). Please see recoup vignettes 
    # for further demonstrations.
    test.in <- list(
        WT_H4K20me1=list(
            id="WT_H4K20me1",
            name="WT H4K20me1",
            file=system.file("extdata",
                "WT_H4K20me1_50kr.bam", 
                package="recoup"),
            format="bam",
            color="#EE0000"
        ),
        Set8KO_H4K20me1=list(
            id="Set8KO_H4K20me1",
            name="Set8KO H4K20me1",
            file=system.file("extdata", 
                "Set8KO_H4K20me1_50kr.bam", 
                package="recoup"),
            format="bam",
            color="#00BB00"
        )
    )
    
    pp=list(
        normalize="none",
        spliceAction="split",
        spliceRemoveQ=0.75
    )
    
    test.in <- preprocessRanges(test.in,pp)