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Last data update: 2014.03.03

R: Coverage histogram

coverage.hist

R Documentation

Coverage histogram

Description

Histogram and cumulative density of target base coverages

Usage

coverage.hist(coverageTarget, col.hist = "lightblue", col.line = "orange", covthreshold, outline = FALSE, breaks = "Sturges", xlab, ylab, main, lwd, ...)

Arguments

`coverageTarget`	`RleList` containing `Rle` vectors of per-target-base coverages for each chromosome, i.e. `coverageTarget` output from `coverage.target`
`col.hist`	histogram color
`col.line`	color of the cumulative density line
`covthreshold`	indicates with dashed vertical and horizontal lines, which fraction of bases has a coverage of at least `covthreshold`; if missing, no dashed lines are drawn
`outline`	if `FALSE`, outliers (according to `boxplot.stats`) are removed before plotting.
`breaks`	number of cells for the histogram, or string naming an algorithm to compute the number of cells, or function to compute the number of cells, or vector giving the breakpoints between histogram cells (see `?hist`) but the latter option only with equidistant breakpoints
`xlab, ylab`	x- and y-axis labels
`main`	plot title
`lwd`	line width
`...`	further graphical parameters, passed to `plot(histogram)`

Value

Histogram of read coverages for bases within the target. Additionally, a line and the right axis indicate the cumulative fraction of target bases with coverage of at least x. If option covthreshold is specified, red dashed lines highlight the cumulative fraction of target bases with at least the specified coverage.

Author(s)

Manuela Hummel m.hummel@dkfz.de

Examples

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## calculate per-base coverages
Coverage <- coverage.target(reads, targets, perBase=TRUE)

## coverage histogram
coverage.hist(Coverage$coverageTarget, covthreshold=8)

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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> library(TEQC)
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: IRanges
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: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: hwriter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TEQC/coverage.hist.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coverage.hist
> ### Title: Coverage histogram
> ### Aliases: coverage.hist
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## get reads and targets
> exptPath <- system.file("extdata", package="TEQC")
> readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
> reads <- get.reads(readsfile, idcol=4, skip=0)
[1] "read 19546 sequenced reads"
> targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
> targets <- get.targets(targetsfile, skip=0)
[1] "read 50 (non-overlapping) target regions"
Warning message:
the "reduce" method for RangedData object is deprecated 
> 
> ## calculate per-base coverages
> Coverage <- coverage.target(reads, targets, perBase=TRUE)
> 
> ## coverage histogram
> coverage.hist(Coverage$coverageTarget, covthreshold=8)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>