Calculate coverage in a set of reference genomic regions (ChIP-Seq or unspliced mode)

Description

This function fills the coverage field in the main input argument in recoup function.

Usage

    coverageRef(
        input, 
        genomeRanges, 
        region = c( "tss", "tes", "genebody", "custom"),
        flank = c(2000, 2000),
        strandedParams = list(strand=NULL, ignoreStrand=TRUE),
        bamParams = NULL,
        rc = NULL
    )

Arguments

Value

Same as input with the ranges fields filled.

Author(s)

Panagiotis Moulos

Examples

# Load some data
data("recoup_test_data",package="recoup")

# Calculate coverages
testGenomeRanges <- makeGRangesFromDataFrame(df=test.genome,
    keep.extra.columns=TRUE)
test.input <- coverageRef(
    test.input, 
    genomeRanges=testGenomeRanges, 
    region="tss",
    flank=c(2000,2000)
)

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/coverageRef.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coverageRef
> ### Title: Calculate coverage in a set of reference genomic regions
> ###   (ChIP-Seq or unspliced mode)
> ### Aliases: coverageRef
> 
> ### ** Examples
> 
> # Load some data
> data("recoup_test_data",package="recoup")
> 
> # Calculate coverages
> testGenomeRanges <- makeGRangesFromDataFrame(df=test.genome,
+     keep.extra.columns=TRUE)
> test.input <- coverageRef(
+     test.input, 
+     genomeRanges=testGenomeRanges, 
+     region="tss",
+     flank=c(2000,2000)
+ )
Calculating tss coverage for WT H4K20me1
Calculating tss coverage for Set8KO H4K20me1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>