Visualize GC-Bias of Hybridization

Description

Generates a plot showing the GC-bias of the hybridization.

Usage

plotGCbias(intensity, sequence, main="")

Arguments

Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

See Also

boxplot

Examples

##
sequence <- unlist(lapply(1:50000, function(x) {paste(sample(c("A","T","C","G"),prob=c(0.3,0.3,0.2,0.2),25,replace=TRUE), collapse="")}))
values <- runif(50000,min=-2,max=2)
plotGCbias(values, sequence)

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 '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(Starr)
Loading required package: Ringo
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
Loading required package: affy

Attaching package: 'affy'

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

    probes

Loading required package: affxparser

Attaching package: 'Starr'

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

    plotDensity

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

    plotMA

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

    plotMA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Starr/plot.gcBias.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGCbias
> ### Title: Visualize GC-Bias of Hybridization
> ### Aliases: plotGCbias
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ##
> sequence <- unlist(lapply(1:50000, function(x) {paste(sample(c("A","T","C","G"),prob=c(0.3,0.3,0.2,0.2),25,replace=TRUE), collapse="")}))
> values <- runif(50000,min=-2,max=2)
> plotGCbias(values, sequence)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>