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# args.addOptionS("o","outFile","outFilePrefix",1,"Prefix for the output files.");
# args.addOptionS("p","parameters","parFileName",1,"File containing estimated hyperparameters.");
# args.addOptionB("s","samples","samples",0,"Produce samples of condition mean expression apart from PPLR and confidence.");
# args.addOptionD("l","lambda0","lambda0",0,"Parameter lambda_0.",LAMBDA_0);
# args.addOptionD("c","confidencePerc","cf",0,"Percentage for confidence intervals.", 5);
estimateDE <- function( conditions, outFile, parFile, lambda0=NULL, samples=NULL, confidencePerc=NULL, verbose=NULL, norm=NULL, seed=NULL, pretend=FALSE ){
## unlist norm
norm <- unlist(norm);
args <- c('estimateDE', unlist(conditions[[1]]));
## parse other conditions
for(i in 2:length(conditions)){
args <- c(args, 'C', unlist(conditions[[i]]));
}
args <- c(args, '--outPrefix', outFile , '--parameters', parFile);
if (!is.null(lambda0)) {
args <- c(args, '--lambda0', lambda0)
}
if (!is.null(samples) && (samples)) {
args <- c(args, '--samples')
}
if (!is.null(confidencePerc)) {
args <- c(args, '--confidenceInterval', confidencePerc)
}
if (!is.null(verbose) && (verbose)) {
args <- c(args, '--verbose')
}
if (!is.null(norm)) {
if(length(unlist(conditions)) != length(norm)){
stop("The number of normalization constants has to match the number of sample files.");
}
args <- c(args, '--norm', paste(norm, collapse=","));
}
if (!is.null(seed)) {
args <- c(args, '--seed', seed)
}
if(pretend){
writeLines(.specialPaste(args))
}else{
argc <- length(args);
##dyn.load(paste("src/estimateDE", .Platform$dynlib.ext, sep=""))
result <- .C("_estimateDE", as.integer(argc), as.character(args))
}
}
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