Man pages for explodecomputer/simulateGP
Functions for simulating genotype-phenotype relationships

add_uAdd confounder variables and their instruments
allele_frequencyEstimate allele frequency from SNP
ascertain_samplesAscertain some proportion of cases and controls from binary...
choose_effectsGet vector of effects that explain some amount of variance
contingencyObtain 2x2 contingency table from marginal parameters and...
create_systemWrapper for simulation pipeline
estimate_system_effectsEstimate the effects of all SNPs on all phenotypes
expected_gwasFor known effect size, sample size and variances, what is the...
fast_assocGet summary statistics in simple linear regression
get_effsGet effs for two traits and make dat format
get_population_allele_frequencyEstimate the allele frequency in population from case/control...
gwasPerform association of many SNPs against phenotype
gx_to_gpTranslate risk from liability to probability scale
init_parametersChoose initial parameters for direct effects on X and Y
lor_to_rsqEstimate proportion of variance of liability explained by SNP...
make_datOrganise outputs from 'gwas' into harmonised dat format
make_genoCreate genotype matrix
make_mvdatTake several exposures and one outcome and make the data...
make_phenSimulate variable based on the influences of other variables
range01Scale variable to have range between 0 and 1
recode_datRecode data to make every effect on x positive
recode_dat_interceptIntercept recoding to have every effect on x positive
recode_dat_simpleSimple recoding to have every effect on x positive
risk_cross_plotPlot liability vs probability disease risk
risk_simulationMake simulation to compare disease and liability scales
sample_system_effectsSample the actual effects based on initial parameters
simulate_populationSimulate individual level data from initial parameters
y_to_binaryConvert continuous trait to binary
explodecomputer/simulateGP documentation built on Nov. 18, 2018, 1:14 p.m.