flag.arrayCGH: Apply a flag to an arrayCGH

Description

Function flag$FUN is applied to a flag object for normalization

Usage

flag.arrayCGH(flag, arrayCGH)

Arguments

flag

an object of type 'flag'

arrayCGH

an object of type arrayCGH

Value

An object of class arrayCGH, which corresponds to the return value of flag$FUN if flag$char is null, and to the input arrayCGH object with spots given by flag$FUN flagged with flag$char

Details

Optional arguments in flag$args are passed to flag$FUN

Examples

Run this code

data(spatial)
data(flags)

gradient$arrayValues$LogRatioNorm <- gradient$arrayValues$LogRatio
## flag spots with no available position on the genome
gradient <- flag.arrayCGH(position.flag, gradient)

## flag spots corresponding to low poor quality clones
gradient <- flag.arrayCGH(val.mark.flag, gradient)

## flag spots excluded by Genepix pro
gradient <- flag.arrayCGH(spot.flag, gradient)

## flag local spatial bias zones
## Not run: gradient <- flag.arrayCGH(local.spatial.flag, gradient)

## correct global spatial bias
gradient <- flag.arrayCGH(global.spatial.flag, gradient)

## flag spots with low signal to noise
gradient <- flag.arrayCGH(SNR.flag, gradient)

## flag spots with extremely high log-ratios
gradient <- flag.arrayCGH(amplicon.flag, gradient)

## flag spots with poor within replicate consistency
gradient <- flag.arrayCGH(replicate.flag, gradient)

## flag spots corresponding to clones for which all other spot
## replicates have already been flagged  
gradient <- flag.arrayCGH(unique.flag, gradient)

summary.factor(gradient$arrayValues$Flag)