Based on parameters provided, this function sets the name for the phenotype simulation. It carries out compatibiltiy checks of the specifie parameters and checks for any missing information.
setModel(genVar = NULL, h2s = NULL, theta = 0.8, h2bg = NULL, eta = 0.8, noiseVar = NULL, delta = NULL, gamma = 0.8, rho = NULL, phi = NULL, alpha = 0.8, pcorr = 0.6, pIndependentConfounders = 0.4, pTraitIndependentConfounders = 0.2, pIndependentGenetic = 0.4, pTraitIndependentGenetic = 0.2, proportionNonlinear = 0, cNrSNP = NULL, NrConfounders = 10, verbose = TRUE)
genVar | Total genetic variance [double]. |
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h2s | Proportion [double] of variance of genetic variant effects. |
theta | Proportion [double] of variance of shared genetic variant effects. |
h2bg | Proportion [double] of variance of infinitesimal genetic effects i.e. correlation introduced by sample kinship). |
eta | Proportion [double] of variance of shared infinitesimal genetic effects. |
noiseVar | Total noise variance [double]. |
delta | Proportion [double] of variance of non-genetic covariate effect. |
gamma | Proportion [double] of variance of shared non-genetic covariate effects. |
rho | Proportion [double] of variance of correlated noise effects. |
phi | Proportion [double] of variance of observational noise effects. |
alpha | Proportion [double] of variance of shared observational noise effect. |
pcorr | Correlation [double] between phenotypes. |
pIndependentConfounders | Proportion [double] of non-genetic covariate to have a trait-independent effect. |
pTraitIndependentConfounders | Proportion [double] of traits influenced by independent non-genetic covariate effects. |
pIndependentGenetic | Proportion [double] of genetic variant effects to have a trait-independent fixed effect. |
pTraitIndependentGenetic | Proportion [double] of traits influenced by independent genetic variant effects. |
proportionNonlinear | [double] proportion of the phenotype to be non- linear |
cNrSNP | Number [integer] of causal SNPs; used as genetic variant effects. |
NrConfounders | Number [integer] of non-genetic covariates; used as non-genetic covariate effects. |
verbose | [boolean]; If TRUE, progress info is printed to standard out. |
Named list containing the genetic model (modelGenetic), the noise model (modelNoise) and the input parameters (h2s, h2bg, noiseVar, rho, delta, phi, gamma, theta, eta, alpha, pcorr, proportionNonlinear). Model options are: modelNoise: "noNoise", "noiseFixedOnly", "noiseBgOnly", "noiseCorrelatedOnly", "noiseFixedAndBg","noiseCorrelatedAndBg", "noiseFixedAndCorrelated", "noiseFixedAndBgAndCorrelated" modelGenetic: "noGenetic","geneticBgOnly", "geneticFixedOnly", "geneticFixedAndBg"
#genetic fixed effects only model <- setModel(genVar=1, h2s=1)#>#>#>#>#>#>#>#>#>#>#genetic fixed and bg effects model <- setModel(genVar=1, h2s=0.01)#>#>#>#>#>#>#>#>#>#>#>#>#genetic and noise fixed effects only model <- setModel(genVar=0.4, h2s=1, delta=1)#>#>#>#>#>#>#>#>#>#>#>#>#>#>#>