Usage
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)
Arguments
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