R/quality.R

In MANOR: CGH Micro-Array NORmalization

## 'qscore' objects: class and methods

## Copyright (C) 2004 Institut Curie
## Author(s): Pierre Neuvial, Isabel Brito (Institut Curie) 2004
## Contact: manor@curie.fr


### create a qscore object
to.qscore <- function(FUN, name=NULL, args=NULL, label=NULL, dec=3)
{
    qs <- list(FUN=FUN, name=name, args=args, label=label, value=NULL, dec=dec)
    class(qs) <- "qscore"
    qs
}

### compute quality scores for a given arrayCGH
qscore.arrayCGH <- function(qscore, arrayCGH) {
    formals(qscore$FUN) <- c(alist(arrayCGH=), qscore$args)
    qscore$FUN(arrayCGH)
}

qscore.summary.arrayCGH <- function(arrayCGH, qscore.list) {
    score <- NULL
    name <- NULL
    label <- NULL
    for (i in 1: length(qscore.list)) {
        qs <- qscore.list[[i]]
        dec <- qs$dec
        score <- c(score, round(qscore.arrayCGH(qs, arrayCGH)*10^dec)/(10^dec))
        name <- c(name, qs$name)
        label <- c(label, qs$label)
    }
    data.frame(name=name, label=label, score=score)
}