Supplemental Material for Mott et al., 2020

# The function CFW.example() will download public data from Nicod et al 2016 Nature Genetics
# That paper analyses outbred CFW mice for many traits, see http://outbredmice.org.
# The function will by default download genotype dosages just for chromosome 11
# and the phenotypes for Platelets (after correction for covariates).
# These data are chosen because there is a QTL for Platelets on chr11
# (see http://mtweb.cs.ucl.ac.uk/qtls/Haem.PLT_chr.11.97045910.pdf)
# It will save these data in a Rdata object D that is organised appropriately for
# encryption and analysis by other functions in this file.
# It then simulates an approprately sized encryyption matrix and
# performs association mapping using both original and encrypted data.
# It also computes diagnostic plots and statistics exploring the
# degree of randomness in the encrypted data (evaluated as the correlation
# between the orioginal and encrypted dosages), and the concordance betgween the
# logP values of the association statistics

# A pdf file of diagnostic plots called "chr11.PLT.pdf"

# Text output should be:
# > CFW.example(seed = 928349)
# Haem.PLT gwas mean diff 0.006406253 max diff 0.03775242
# Min. 1st Qu. Median Mean 3rd Qu. Max.
# 2.450e-06 1.949e-03 3.945e-03 6.406e-03 8.030e-03 3.775e-02
# correlation of genotypes
# Min. 1st Qu. Median Mean 3rd Qu. Max.
# 1.330e-06 7.942e-03 1.676e-02 2.061e-02 2.989e-02 8.331e-02
# correlation of phenotypes
# [,1]
# [1,] 0.01833442