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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(recoup)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: ggplot2
Loading required package: ComplexHeatmap
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/recoup/preprocessRanges.Rd_%03d_medium.png", width=480, height=480)
> ### Name: preprocessRanges
> ### Title: Read and preprocess BAM/BED files to GRanges
> ### Aliases: preprocessRanges
> 
> ### ** 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)
Reading sample WT H4K20me1
Reading sample Set8KO H4K20me1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>