HEGP.examples.R (14.35 kB)

Example Software in R for Homomorphic Encryption

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posted on 28.02.2020 by Richard Mott
# 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

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