setRectRegion {affyContam} | R Documentation

## 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

`x` | AffyBatch instance
`chip` | sample index
`xinds` | x coordinates to be contaminated
`yinds` | y coordinates to be contaminated
`vals` | values to be assigned to rectangle elements
`center` | geometric center of circle to be altered
`rad` | radius of circle to be altered, in xy units of the chip addressing system used by xy2indices in the cdf package
`valgen` | function of parameter n that generates n values to be inserted in the altered region

### 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)

[Package affyContam version 1.0.0 Index]