combineFiles: Combine the X and Y intensity scores and the assigned dosage...

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Combine the X and Y intensity scores and the assigned dosage in one file

Description

This function combines the X and Y intensity values from the fitPoly input with the geno (assigned dosage) from the fitPoly scores output. Useful for producing XY scatterplots with samples colored according to the assigned dosage.

Usage

combineFiles(XYdata, scores, controls=character(0))

Arguments

XYdata	data.frame with (at least) columns MarkerName, SampleName, X, Y (if present, R and ratio are also copied)
scores	data.frame with scores produced by the fitMarkers function of package fitPoly. It has columns MarkerName and SampleName that are subsets of MarkerName and SampleName in the XYdata, and at least a column geno
controls	a character vector of sample names. The geno (dosage) value of these samples is set to NA

Value

a dataframe with columns MarkerName, SampleName, X, Y (and R and ratio if these columns were present in XYdata), and geno, with all markers and samples from XYdata. The value of geno is set to NA for all MarkerName / sample combinations not present in scores, and for all samples in controls.

fitPoly documentation built on April 3, 2025, 8:58 p.m.