XY_data.txt contains PLINK "F-statistics", X chromosome heterozygosity, and Y chromosome missingness of individuals in the TRAINING SET (subjects in prostate cancer and ovarian cancer GWAS) that are used to fit a logistic regression model.

1) Download seXY.R (or seXY_commandline.R) and XY_data.txt. 

2) Obtain TEST SET genotype data from X and Y chromosomes in either PLINK format (*.ped) or GenomeStudio matrix format (*.txt).

3) Enter the required inputs for seXY.R (header lines) and run code in R. Alternatively, seXY_commandline.R can be run from the commandline in the same directory as input files.
Ex 1. "Rscript --vanilla seXY_commandline.R PLINK GWAS_X.ped GWAS_Y.ped"
Ex 2. "Rscript --vanilla seXY_commandline.R GS GWAS_X.txt GWAS_Y.txt"