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Last data update: 2014.03.03

R: Show Array Mask

showArrayMask

R Documentation

Show Array Mask

Description

Function to display beads masked by BASH. The masked beads are assumed to have a weight of 0 in the specified weights column.

Usage


showArrayMask(BLData,array = 0, override = FALSE, wtsName = "wts", transFun = logGreenChannelTransform, outlierFun = illuminaOutlierMethod, horizontal=TRUE)

Arguments

`BLData`	A BeadLevelList object.
`override`	Logical. Plotting a large mask can cause slowdown problems. By default, if more than 200 000 beads are masked, the current mask will not be plotted. You can force the mask to be plotted by setting this argument to `TRUE`, however beware as this may cause slower systems to freeze.
`wtsName`	name under which the bead weights are stored
`array`	numeric index of the array to plot
`transFun`	function to transform intensities prior to calculating outliers
`outlierFun`	function to remove outliers
`horizontal`	if TRUE the resulting image is plotting with the longest edge along the x axis

Details

showArrayMask plots the beads on an array that have been assigned a weight of 0 by BASH in red, and beads determined to be outliers in black.

Value

None returned

Author(s)

Jonathan Cairns and Mark Dunning

Examples


if(require(beadarrayExampleData)){

  data(exampleBLData)

  showArrayMask(exampleBLData,2)

}

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(beadarray)
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: 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: ggplot2
Welcome to beadarray version 2.22.2
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarray/showArrayMask.Rd_%03d_medium.png", width=480, height=480)
> ### Name: showArrayMask
> ### Title: Show Array Mask
> ### Aliases: showArrayMask
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> if(require(beadarrayExampleData)){
+ 
+   data(exampleBLData)
+ 
+   showArrayMask(exampleBLData,2)
+ 
+ }
Loading required package: beadarrayExampleData
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>