This function uses a reference set to test the unknown samples
The unknown samples needs to be a binned counts file which can
be created using the makeBinnedCountsFile function.
rapidr.ref object which contains the baselines and
the corrections used to create the baselines
unknowns.counts.file
file name of the file with the binned counts
of the unknowns, first column needs to be the sampleID, first row
needs to be the chromosome names of each bin
gcContentFile
file name of a .Rdata object which contains
information on GC content in the genome
masked.counts.file
optional file of the binned counts after masking
combined.counts.fname
file name to write to for the combined counts
per chromosome
Value
data.frame with z-scores for chr21, chr18, chr13, and the fetal sex
which can be male, female or monosomy X. For males, there is also
an estimate of the fetal fraction using the deficit of chrX