flag {MANOR} | R Documentation

## Create an object of type flag

### Description

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)

### Usage

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

### Arguments

`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

### Details

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`.

### Value

An object of class `flag`.

### Note

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

### Author(s)

Pierre Neuvial, manor@curie.fr.

### See Also

`flag.arrayCGH`, `norm.arrayCGH`

### Examples

    ### 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

[Package MANOR version 1.14.0 Index]