to.flag: Create an object of type flag
In MANOR: CGH Micro-Array NORmalization

Description Usage Arguments Details Value Note Author(s) See Also Examples

A flag object is a list which contains essentially a function (flag action) and a character, optionally arguments to be passed to the function. We make the distinction between two different flag types, corresponding to two different purposes: - permanent flags identify poor quality spots or clones and remove them from further analysis (eg spots with low signal to noise ratio) - temporary flags identify spots or clones that have not to be taken into account for the computation of a (scaling) normalization coefficient (eg X chromosome in case of sex mismatch)

1	to.flag(FUN, char=NULL, args=NULL, type="perm.flag", label=NULL)

`FUN`	a R function to be applied to an `arrayCGH`, and optionally other arguments. If char is not NULL, must return a list of spots (lines of `arrayCGH$arrayValues`) to be flagged out; if `char==NULL`, must return an object of type `arrayCGH`
`char`	a character value to identify flagged spots; defaults to NULL
`args`	a list of further arguments to be passed to `FUN`; defaults to NULL (ie `arrayCGH` is the only argument to `FUN`)
`type`	a character value defaulting to "perm.flag" which makes the distinction between permanent flags (type="perm.flag") and temporary flags (type="temp.flag")
`label`	a character value for flag labelling

If flag$char is null, flag$FUN is supposed to return a arrayCGH object; if it is not null, flag$FUN is supposed to return a list of spots to be flagged with flag$char.

An object of class flag.

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

Pierre Neuvial, manor@curie.fr.

flag.arrayCGH, norm.arrayCGH

### creation of a permanent flag:
## flag spots with low signal to noise ratios
SNR.FUN <- function(arrayCGH, snr.thr)
    which(arrayCGH$arrayValues$F2 < arrayCGH$arrayValues$B2+log(snr.thr, 2))
SNR.char <- "B"
SNR.flag <- to.flag(SNR.FUN, SNR.char, args=alist(snr.thr=3))

### creation of a permanent flag returning an arrayCGH object:
## correct log-ratios for spatial trend

global.spatial.FUN <- function(arrayCGH, var)
  {
    Trend <- arrayTrend(arrayCGH, var, span=0.03, degree=1,
iterations=3, family="symmetric")
    arrayCGH$arrayValues[[var]] <- Trend$arrayValues[[var]]-Trend$arrayValues$Trend
    arrayCGH
  }
global.spatial.flag <- to.flag(global.spatial.FUN, args=alist(var="LogRatio"))

### creation of a temporary flag:
## exclude sexual chromosomes from signal scaling
chromosome.FUN <- function(arrayCGH, var)
  which(!is.na(match(as.character(arrayCGH$arrayValues[[var]]), c("X", "Y"))))
chromosome.char <- "X"
chromosome.flag <- to.flag(chromosome.FUN, chromosome.char, type="temp.flag",
args=alist(var="Chromosome")) 

data(spatial)

SNR.flag$args$snr.thr <- 3                   ## set SNR threshold
gradient <- flag.arrayCGH(SNR.flag, gradient)    ## apply SNR.flag to array CGH

gradient <- flag.arrayCGH(global.spatial.flag, gradient)

gradient <- flag.arrayCGH(chromosome.flag, gradient)

summary.factor(gradient$arrayValues$Flag)   ## permanent flags
summary.factor(gradient$arrayValues$FlagT)  ## temporary flags