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## 'flag' objects: class and methods
## Copyright (C) 2004 Institut Curie
## Author(s): Pierre Neuvial (Institut Curie) 2004
## Contact: manor@curie.fr
### apply flag function to an arrayCGH
flag.arrayCGH <- function(flag, arrayCGH)
{
formals(flag$FUN) <- c(alist(arrayCGH=), flag$args)
if(!is.null(flag$char))
## flag FUN returns a list of spots
{
w <- flag$FUN(arrayCGH)
if (flag$type=="perm.flag") ## permanent flags
{
if (is.na(match("Flag", names(arrayCGH$arrayValues))))
## add field "Flag" if it does not exist yet
arrayCGH$arrayValues$Flag <- rep("", dim(arrayCGH$arrayValues)[1])
arrayCGH$arrayValues$Flag[w] <- flag$char
}
else ## temporary flags are also kept
{
if (is.na(match("FlagT", names(arrayCGH$arrayValues))))
## add field "FlagT" if it does not exist yet
arrayCGH$arrayValues$FlagT <- rep("", dim(arrayCGH$arrayValues)[1])
arrayCGH$arrayValues$FlagT[w] <- flag$char
}
}
else
## flag.FUN returns a new arrayCGH object
arrayCGH <- flag$FUN(arrayCGH)
arrayCGH
}
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