HEGP.example.R# Author: Richard Mott, UCL Genetics Institute.# (C) 2019 Richard Mott# 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: # > source("HEGP.examples.R")# > CFW.example(mixed.model=TRUE)# estimated heritability 0.02534315# Built kinship dim 1329 1329# estimated heritability 0.025049# gwas logP mean diff 0.003140902 max diff 0.02634605 cor 0.9999849# Min. 1st Qu. Median Mean 3rd Qu. Max.# 7.400e-08 1.103e-03 2.158e-03 3.141e-03 3.865e-03 2.635e-02# correlation of plaintext and ciphertext 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 plaintext and ciphertext phenotypes# [,1]# [1,] 0.01833442# [1] 1