Calculate coverages over a genomic region

Description

This function returns a coverage list for the genomic regions in mask argument. Generally it should not be used alone and is intended for internal use, although it is useful for calculating stand-alone coverages.

Usage

    calcCoverage(input, mask, strand = NULL,
        ignore.strand = TRUE, rc = NULL)

Arguments

Details

input contains the short reads in one of the formats described in the arguments section. When input is a list, this list should contain one member per chromosome of the organism of interest.

mask contains the genomic regions over which the coverage will be calculated from the input reads. When calculating RNA-Seq profiles, mask must be a named GRangesList where each member represents the exons of the respective gene.

Value

A list of Rle objects representing the genomic coverages of interest.

Author(s)

Panagiotis Moulos

Examples

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

# Calculate coverage Rle
mask <- makeGRangesFromDataFrame(df=test.genome,
    keep.extra.columns=TRUE)
small.cov <- calcCoverage(test.input[[1]]$ranges,mask)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> 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/calcCoverage.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calcCoverage
> ### Title: Calculate coverages over a genomic region
> ### Aliases: calcCoverage
> 
> ### ** Examples
> 
> # Load some data
> data("recoup_test_data",package="recoup")
> 
> # Calculate coverage Rle
> mask <- makeGRangesFromDataFrame(df=test.genome,
+     keep.extra.columns=TRUE)
> small.cov <- calcCoverage(test.input[[1]]$ranges,mask)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>