testUnknowns: testUnknowns

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

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

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.