Nothing
###
### $Id: mkRPPATumorDataset.R 947 2015-01-21 17:44:54Z proebuck $
### (Re)creates 'rppaTumor' 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)
}
##
## Tumor data with 3 antibodies
##
extdata.dir <- system.file("extdata", package="SuperCurveSampleData")
rawdata.dir <- file.path(extdata.dir, "rppaTumorData")
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)
## :BUG: last two lines of layout info file look hinky.
layoutinfofile <- "layoutInfo.tsv"
slidedesignfile <- "slidedesign.tsv"
assign(design <- "tDesign",
RPPADesign(rppa <- get(rppas[1]),
grouping="blockSample",
center=TRUE,
aliasfile=layoutinfofile,
designfile=slidedesignfile,
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)
})
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