Visualize digestion fragments with a histogram

Description

This function is a small convenience function to plot the results of simulateDigestion as a histogram. Minimum and maximum fragment lengths can be specified to visualize a specified interval of the fragment data.

Usage

  drawDigestionFragmentHistogram(fragments, minLength = 0, maxLength = 10000)

Arguments

Value

Histogram plot of the fragment data

Author(s)

Carolin Walter

Examples

  shortTestGenome = "ATCCATGTAGGCTAAGTACACATGTTAAGGTACAGTACAATTGCACGATCAT"
  fragments = simulateDigestion("catg", "gtac", shortTestGenome)
  drawDigestionFragmentHistogram(fragments)

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
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> library(Basic4Cseq)
Loading required package: Biostrings
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,
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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

Loading required package: S4Vectors
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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: GenomicAlignments
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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")'.

Loading required package: Rsamtools
Loading required package: caTools

Attaching package: 'caTools'

The following object is masked from 'package:IRanges':

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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/drawDigestionFragmentHistogram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: drawDigestionFragmentHistogram
> ### Title: Visualize digestion fragments with a histogram
> ### Aliases: drawDigestionFragmentHistogram
> ###   drawDigestionFragmentHistogram,data.frame-method
> ### Keywords: drawDigestionFragmentHistogram
> 
> ### ** Examples
> 
>   shortTestGenome = "ATCCATGTAGGCTAAGTACACATGTTAAGGTACAGTACAATTGCACGATCAT"
>   fragments = simulateDigestion("catg", "gtac", shortTestGenome)
>   drawDigestionFragmentHistogram(fragments)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>