Description Usage Arguments Details Value See Also Examples

View source: R/simCNVdataCaseCon.R

This function simulates intensity for a CNV within cases and control groups for different scenarios

1 2 | ```
simCNVdataCaseCon(n0, n1, w0, or, mu.surrog0, sd.surrog0, mu.surrog1 = mu.surrog0,
sd.surrog1 = sd.surrog0, random = TRUE)
``` |

`n0` |
number of controls simulated |

`n1` |
number of cases simulated |

`w0` |
vector of proportions of copy number status in controls |

`or` |
a vector of odds ratio for one, two,... copies respect to zero copies |

`mu.surrog0` |
vector of means of CNV intensity signal, per copy number status, in control group |

`sd.surrog0` |
vector of standard deviations of CNV intensity signal, per copy number status, in control group |

`mu.surrog1` |
vector of means of CNV intensity signal, per copy number status, in control group |

`sd.surrog1` |
vector of standard deviations of CNV intensity signal, per copy number status, in control group |

`random` |
A logical value. TRUE means that individuals (rows) are randomly permuted, and FALSE means that simulated 'data.frame' contains controls first and then cases. Default value is TRUE |

This function is useful to calculate the power of association models in a case control study design under different scenarios ,e.g. setting different degrees of association (odds ratios), considering different degrees of uncertainty controlled by the distribution of intensity signal data, i.e. mean `mu.surrog`

, standard deviation `sd.surrog`

and proportion `w`

, etc.

Data frame with individual simulated data per row and with the following variables:

`resp` |
Trait (response) variable with 0 or 1 if the individual is a control or a case respectively |

`surrog` |
Signal intensity following a mixture of normals with means, standard deviations
and proportions specified by |

`cnv` |
True copy number status |

`simCNVdataBinary`

,
`simCNVdataNorm`

,
`simCNVdataPois`

,
`simCNVdataWeibull`

,
`cnv`

,
`CNVassoc`

1 2 3 4 5 6 7 8 9 10 11 | ```
maf<-0.3
set.seed(123)
simData<-simCNVdataCaseCon(n0=1000, n1=1000, mu.surrog0=c(0,0.5,1), sd.surrog0=rep(0.15,3),
mu.surrog1=c(0,0.5,1), sd.surrog1=rep(0.15,3),
w0=c((1-maf)^2,2*maf*(1-maf), maf^2), or=c(1.3,1.3^2),
random = FALSE)
CNV<-cnv(simData$surrog,mix.method="EMmixt")
getQualityScore(CNV,type="CNVtools")
mod<-CNVassoc(resp~CNV,data=simData,family="binomial")
CNVtest(mod)
summary(mod)
``` |

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