Description Usage Arguments Value Examples

View source: R/createphenotypeFunctions.R

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
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]. |

`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"

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