flag.arrayCGH {MANOR} | R Documentation |
Function flag$FUN
is applied to a flag
object for
normalization
flag.arrayCGH(flag, arrayCGH)
flag |
an object of type 'flag' |
arrayCGH |
an object of type arrayCGH |
Optional arguments in flag$args
are passed to
flag$FUN
An object of class arrayCGH
, which corresponds to the return
value of flag$FUN
if flag$char
is null, and to the
input arrayCGH
object with spots given by flag$FUN
flagged with flag$char
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Pierre Neuvial, manor@curie.fr.
data(spatial) data(flags) gradient$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)