Plot island depth distribution

Description

Plots the distribution of island depths using points for the observed islands and a line for the Poisson estimate of the noise. Useful for choosing a depth corresponding to a desired FDR.

Usage

islandDepthPlot(x, maxDepth = 20L)

Arguments

Author(s)

D. Sarkar, M. Lawrence

See Also

peakCutoff for calculating a cutoff value for an FDR.

Examples

data(cstest)
cov <- coverage(resize(cstest$ctcf, width=200))
islandDepthPlot(cov)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(chipseq)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
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    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
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    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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Attaching package: 'S4Vectors'

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    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
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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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chipseq/islandDepthPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: islandDepthPlot
> ### Title: Plot island depth distribution
> ### Aliases: islandDepthPlot
> 
> ### ** Examples
> 
> data(cstest)
> cov <- coverage(resize(cstest$ctcf, width=200))
> islandDepthPlot(cov)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>