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# args.addOptionS("o","outFile","outFileName",1,"Name of the output file.");
# args.addOptionB("l","log","log",0,"Use logged values.");
# args.addOptionS("t","type","type",0,"Type of variance, possible values: [sample,sqDif] for sample variance or squared difference.","sample");
getMeanVariance <- function(sampleFiles, outFile, log=NULL, type=NULL, verbose=NULL, norm=NULL, pretend=FALSE){
## we want sampleFiles and norm to be a vector
sampleFiles <- unlist(sampleFiles);
norm <- unlist(norm);
args <- c('getVariance', sampleFiles, '--outFile', outFile);
if ((!is.null(log)) && (log)) {
args <- c(args, '--log')
}
if (!is.null(type)) {
args <- c(args, '--type', type)
}
if (!is.null(verbose) && (verbose)) {
args <- c(args, '--verbose')
}
if (!is.null(norm)) {
if(length(sampleFiles) != length(norm)){
stop("The number of normalization constants has to match the number of sample files.");
}
args <- c(args, '--norm', paste(norm, collapse=","));
}
if(pretend){
writeLines(.specialPaste(args))
}else{
argc <- length(args);
## dyn.load(paste("src/getVariance", .Platform$dynlib.ext, sep=""));
result <- .C("_getVariance", as.integer(argc), as.character(args));
}
}
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