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Last data update: 2014.03.03

R: Plot the probe length frequency

probeLengthPlot

R Documentation

Plot the probe length frequency

Description

Plot the probe length frequency.

Usage

  probeLengthPlot(xSet, sgrset = 1, chr = NULL, bound.cutoff, probe.max.spacing = 200, xlim.max = 25)

Arguments

`xSet`	object of class ExpressionSet
`sgrset`	integer; specifying which data set to use from the ExpressionSet
`chr`	probes from which chromosome to be used, default NULL means all probes
`bound.cutoff`	numeric; threshold above probes are considered “bound”
`probe.max.spacing`	integer; maximum amount of base pairs at which bound probes are condensed into one region.
`xlim.max`	integer; maximum number of probes plotted along the x-axsis

Details

Plot the probe length frequency per regions based on a bound.cutoff value.

Value

Plot of frequency of the number of probes within bound regions

Author(s)

Bettina Fischer

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  probeLengthPlot(SGR, sgrset=1, chr=NULL, bound.cutoff=1.2, probe.max.spacing=200, xlim.max=50)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(SimBindProfiles)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SimBindProfiles/probeLengthPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: probeLengthPlot
> ### Title: Plot the probe length frequency
> ### Aliases: probeLengthPlot
> 
> ### ** Examples
> 
>   dataPath <- system.file("data",package="SimBindProfiles")
>   load(file.path(dataPath,"SGR.RData"))
>   probeLengthPlot(SGR, sgrset=1, chr=NULL, bound.cutoff=1.2, probe.max.spacing=200, xlim.max=50)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>