preprocessRanges {recoup} | R Documentation

## 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, genome,
            bamRanges=NULL, 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.
`genome` | see the `genome` argument in the main `recoup` function.
`bamRanges` | a `GRanges` object to mask the BAM/BED files to save time and space. If `NULL`, the whole file is read.
`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.

### Author(s)

Panagiotis Moulos

### 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)

[Package recoup version 1.20.1 Index]