createReferenceSetFromCounts: createReferenceSetFromCounts

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

Description

This function creates a reference set from a binned counts file

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

Value

class of rapidr.ref which can then be used to test unknown samples

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