flag.arrayCGH: Apply a flag to an arrayCGH

In MANOR: CGH Micro-Array NORmalization

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

Details

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

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

Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

Author(s)

Pierre Neuvial, [e-mail].

See Also

to.flag, norm.arrayCGH

Examples

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)

MANOR documentation built on Nov. 8, 2020, 6:52 p.m.