createReferenceSetFromCounts: createReferenceSetFromCounts
In RAPIDR: Reliable Accurate Prenatal non-Invasive Diagnosis R package

This function creates a reference set from a binned counts file

createReferenceSetFromCounts(binned.counts.file, outcomes,
  combined.counts.fname = NULL, method = "zscore", gcCorrect = FALSE,
  gcContentFile = NULL, filterBin = TRUE, removeOutlierSamples = FALSE,
  PCA = FALSE, numPC = 10, masked.counts.file = NULL,
  cleaned.binned.counts.fname = NULL)

`binned.counts.file`	file name of the binned counts. The binned counts file should be comma delimited, and the first line need to be the chromosome names of each bin
`outcomes`	data.frame with column names: Dx, Gender, SampleID
`combined.counts.fname`	file name to write to for the combined counts per chromosomes, default is not to write result to file
`method`	either "zscore", "NCV" or "MAD", default is zscore
`gcCorrect`	whether to do gc correction or not (True = do the correction)
`gcContentFile`	file name of a Rdata object with the gcContent data
`filterBin`	whether to filter bins based on unusually high counts and high variance, default is to filter
`removeOutlierSamples`	whether to remove samples which has a low correlation value to the rest of the reference set, default is FALSE
`PCA`	whether to do PCA correction or not (True = do the correction)
`numPC`	number of principal components to discard (default = 10)
`masked.counts.file`	file name of the masked counts file
`cleaned.binned.counts.fname`	file name to write to for the corrected binned counts, default is not to write to file