testUnknowns: testUnknowns

Description Usage Arguments Value

Description

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.

Usage

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testUnknowns(ref.data.set, unknowns.counts.file, gcContentFile = NULL,
  masked.counts.file = NULL, combined.counts.fname = NULL)

Arguments

ref.data.set

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


RAPIDR documentation built on May 1, 2019, 8:18 p.m.