readXY: Read SNP array intensity data
In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

readXY

R Documentation

Read SNP array intensity data

Description

Read SNP array intensity data

Usage

readXY(filename, skip = 9, output = "ratio")

Arguments

`filename`	filename
`skip`	number of lines to skip before the header line with the column names
`output`	One of three options: "ratio","theta","AD"

Details

The first two columns of the tab-delimited input file should be the SNP and Sample ID. Columns labeled "X" and "Y" contain the signal intensities for the two alleles. Use output to specify whether to return the ratio = Y/(X+Y) or theta = atan(Y/X)*2/pi. Option "AD" exports the XY data in the allele depth format for a VCF file ("X,Y"), with the X and Y values multiplied by 100 and rounded to the nearest integer.