R/init.R

In sneumann/xcms-presvnbridge: LC/MS and GC/MS Data Analysis

## .initFindPeaks <- function(all.xcms) {
##
##   assign("findPeaksMethods",
##         substr(all.xcms[grep("findPeaks.\.*", all.xcms)], start+1, 100),
##         envir=as.environment(where))
##
## }


.setXCMSOptions <- function(pkgname,xcms.opt=NA) {

    if (! any(is.na(xcms.opt))) {
        if (class(xcms.opt) != "BioCPkg")
            stop("obviously invalid package options !")

        BioC <- getOption("BioC")
        BioC$xcms <- xcms.opt
        options("BioC"=BioC)
        return()
    }

    ## add xcms specific options
    ## (not unlike what is done in 'affy')
    if (is.null(getOption("BioC"))) {
        BioC <- list()
        class(BioC) <- "BioCOptions"
        options("BioC"=BioC)
    }

    ## all findPeaks methods
    start <- nchar("findPeaks.")
    all.xcms <- ls(asNamespace(pkgname))
    findPeaks.methods <-  substr(all.xcms[grep("findPeaks\\..*", all.xcms)], start+1, 100)

    ## default for the methods
    findPeaks.method <- "matchedFilter"

    ## all groupPeaks methods
    start <- nchar("group.")
    all.xcms <- ls(asNamespace(pkgname))
    group.methods <-  substr(all.xcms[grep("group\\..*", all.xcms)], start+1, 100)

    ## default for the methods
    group.method <- "density"

    ## all groupPeaks methods
    start <- nchar("retcor.")
    all.xcms <- ls(asNamespace(pkgname))
    retcor.methods <-  substr(all.xcms[grep("retcor\\..*", all.xcms)], start+1, 100)

    ## default for the methods
    retcor.method <- "peakgroups"

    ## all fillPeaks methods
    start <- nchar("fillPeaks.")
    all.xcms <- ls(asNamespace(pkgname))
    fillPeaks.methods <-  substr(all.xcms[grep("fillPeaks\\..*", all.xcms)],
                                 start+1, 100)
    ## default method
    fillPeaks.method <- "chrom"

    ## all specDist methods
    start <- nchar("specDist.")
    all.xcms <- ls(asNamespace(pkgname))
    specDist.methods <-  substr(all.xcms[grep("specDist\\..*", all.xcms)],
                                start+1, 100)
    ## default method
    specDist.method <- "meanMZmatch"

    xcms.opt <- list(findPeaks.method=findPeaks.method, findPeaks.methods=findPeaks.methods,
                     group.method=group.method, group.methods=group.methods,
                     retcor.method=retcor.method, retcor.methods=retcor.methods,
                     fillPeaks.method=fillPeaks.method, fillPeaks.methods=fillPeaks.methods,
                     specDist.methods=specDist.methods)

    class(xcms.opt) <- "BioCPkg"

    BioC <- getOption("BioC")
    BioC$xcms <- xcms.opt
    options("BioC"=BioC)
}