inst/util/mkRPPATripleDataset.R

In SuperCurve: RPPA Analysis Package

###
### $Id: mkRPPATripleDataset.R 947 2015-01-21 17:44:54Z proebuck $
### (Re)creates 'rppaTriple' dataset object found in 'data' directory.
###


local({
    ##-------------------------------------------------------------------------
    makeRPPAs <- function(antibody,
                          filename,
                          datadir,
                          xform=function(x) tolower(x)) {
        ## Check argumments
        stopifnot(is.character(antibody) && length(antibody) == 1)
        stopifnot(is.character(filename) && length(filename) == 1)
        stopifnot(is.character(datadir) && length(datadir) == 1)
        stopifnot(is.function(xform))

        ## Begin processing
        assign(varname <- make.names(xform(antibody)),
               RPPA(filename,
                    path=datadir,
                    antibody=antibody),
               envir=environment(makeRPPAs))

        return(varname)
    }


    ##
    ## Triple data with 5 antibodies
    ##

    extdata.dir <- system.file("extdata", package="SuperCurveSampleData")
    rawdata.dir <- file.path(extdata.dir, "rppaTripleData")
    proteinassayfile <- file.path(rawdata.dir, "proteinAssay.tsv")
    proteinassay.df <- read.delim(proteinassayfile)

    rppas <- apply(proteinassay.df,
                   1,
                   function(proteinassay, datadir) {
                       makeRPPAs(proteinassay["Antibody"],
                                 proteinassay["Filename"],
                                 datadir)
                   },
                   rawdata.dir)

    layoutinfofile <- "layoutInfo.tsv"
    ## :TBD: Sample column in layout info file doesn't match those in quantification files 
    ## :TODO: Missing 'slidedesign.tsv' file

    assign(design <- "tripledesign",
           RPPADesign(rppa <- get(rppas[1]),
                      grouping="byRow",
                      controls=list("Buffer",
                                    "Blank"),
                      aliasfile=layoutinfofile,
                      path=rawdata.dir))

    ## Update package data directory
    filename <- sprintf("%s.RData", sub("Data$", "", basename(rawdata.dir)))
    dataset <- file.path(system.file("data", package="SuperCurve"), filename)
    save(list=c(rppas, design),
         file=dataset, 
         compress="xz", 
         compression_level=9)
})