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run1.moss <- function (filename, alpha = 1, c = 0.1, cPrime = 0.0001, q = 0.1, replicates = 5, maxVars = 3, dimens=NULL, k = 2) {
if(missing(filename)) stop("Name of input file must be provided.")
data <- read.table(filename, header=FALSE, sep="\t", stringsAsFactors=FALSE)
if(ncol(data) <= 1)
data <- read.table(filename, header=FALSE, sep=" ", stringsAsFactors=FALSE)
# If user did not provide the 'dimens' vector, we build it
# assuming that all columns have the same number of values,
# except for the last column, which is representing CASE/Control.
if(is.null(dimens)) {
datacol <- dim(data)[2]
dimens <- array(2, datacol)
paramCounter <- apply(data, 2, unique)
i <- 1
#maxlen <- 2
while(i<datacol) {
if(length(unlist(paramCounter[i])) > 2)
dimens[i] <- length(unlist(paramCounter[i]))
i <- i + 1
}
#dimens <- array(maxlen, datacol)
#dimens[datacol] <- 2 # last variable CASE/CONTROL
#print("**************************************")
# print(dimens)
#print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
#print(maxlen)
}
return(MOSS.GWAS(alpha = alpha, c = c, cPrime = cPrime, q = q, replicates = replicates, maxVars = maxVars, data=data, dimens=dimens, k = k))
}
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