[BioC] PEAK PROBABILITY CONTRASTS (PPC) package

[Stephen Nyangoma]

Hi Everyone,
I do not seem to be able to implement the PPC package for MALDI data sets. 
The function

ppc.read.raw.nobatch

calls other functions

ppc.xl.get.names.of.files & ppc.options

that are not given in the package. Can someone out there clarify if I am 
missing something.

I give the function in question below.
###########################
> library(ppc)
> ppc.read.raw.nobatch
function (directory, mz = NULL)
{
    datafiles.list <- ppc.xl.get.names.of.files(directory)
    if (is.null(mz)) {
        pat1 <- read.table(datafiles.list[1])
        mz <- pat1[, 1]
    }
    xtr <- matrix(NA, nrow = length(mz), ncol = length(datafiles.list))
    for (j in 1:length(datafiles.list)) {
        if (ppc.options$debug)
            print(paste("Reading file", datafiles.list[j]))
        temp <- read.table(datafiles.list[j], sep = ",")
        xtr[, j] <- approx(temp[, 1], temp[, 2], xout = mz)$y
    }
    return(list(xtr = xtr, mz = mz, filenames = datafiles.list))
}
<environment: namespace:ppc>
#############################################

Steve.