set a rectangular or circular region in an affybatch to a specified set of values

Description

set a rectangular or circular region in an affybatch to a specified set of values

Usage

setRectRegion(x, chip=1, xinds=251:350, yinds=251:350, vals=10, valgen=NULL)
setCircRegion(x, chip=1, center=c(350,350), rad=100, vals=10, valgen=NULL)
getRectRegion(x, chip=1, xinds=251:350, yinds=251:350)
getCircRegion(x, chip=1, center=c(350,350), rad=100)

Arguments

Value

set* functions return AffyBatch instance with intensities modified as requested

get* functions return numeric vectors of intensities as requested.

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

library(affydata)
data(Dilution)
opar = par(no.readonly=TRUE)
par(mfrow=c(2,2))
hist(Dilution, main="original")
image(Dilution[,1], main="original")
#
# we will contaminate in two ways: thin line at fixed low intensity, and 
# circular blob at moderate random intensity
#
ab = setRectRegion(Dilution, 1, xinds=25:30, yinds=1:620,
  vals=10)
ab = setCircRegion(ab, 1, valgen=function(n){
   rnorm(n, 350,50)})
hist(ab, main="chip 1 contaminated by normal")
image(ab[,1], main="chip 1 contaminated")
ex = getCircRegion(Dilution, 1)
length(ex)
ab = setCircRegion(Dilution, 1, vals=pmin(2*ex,65535))
image(ab[,1], main="chip 1 contaminated by doubling")
par(opar)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(affyContam)
Loading required package: tools
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: affy
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affyContam/setRectRegion.Rd_%03d_medium.png", width=480, height=480)
> ### Name: setRectRegion
> ### Title: set a rectangular or circular region in an affybatch to a
> ###   specified set of values
> ### Aliases: setRectRegion setCircRegion getRectRegion getCircRegion
> ### Keywords: models
> 
> ### ** Examples
> 
> library(affydata)
> data(Dilution)
> opar = par(no.readonly=TRUE)
> par(mfrow=c(2,2))
> hist(Dilution, main="original")

Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> image(Dilution[,1], main="original")
> #
> # we will contaminate in two ways: thin line at fixed low intensity, and 
> # circular blob at moderate random intensity
> #
> ab = setRectRegion(Dilution, 1, xinds=25:30, yinds=1:620,
+   vals=10)
> ab = setCircRegion(ab, 1, valgen=function(n){
+    rnorm(n, 350,50)})
> hist(ab, main="chip 1 contaminated by normal")
> image(ab[,1], main="chip 1 contaminated")
> ex = getCircRegion(Dilution, 1)
> length(ex)
[1] 31397
> ab = setCircRegion(Dilution, 1, vals=pmin(2*ex,65535))
> image(ab[,1], main="chip 1 contaminated by doubling")
> par(opar)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>