Description Usage Arguments Details Value Author(s) References See Also Examples

Simulates SNP data with genotypes coded by 0, 1 and 2 as well as a binary and a continuous covariate, together with case-control status specified by logistic regression.

1 2 | ```
generateSNPs(n, gene.no, block.no, block.size, p.same,
p.different = NULL, p.minor, n.sample, SNPtoBETA)
``` |

`n` |
an integer specifying the number of observations (cases and controls with 1:1 match) that should be generated. |

`gene.no` |
an integer specifying the number of genes that should be generated. |

`block.no` |
an integer specifying the number of blocks per gene. |

`block.size` |
an integer specifying the number of SNPs per block. |

`p.same` |
either a numeric value specifying the probability for neighborhood SNPs within a block or a numeric vector of length |

`p.different` |
a numeric value specifying the probability for neighborhood blocks within a gene which is used if |

`p.minor` |
a vector of length |

`n.sample` |
an integer specifying the number of simulated subjects from which the observations (case-control status) |

`SNPtoBETA` |
a matrix of non-negative numeric values of dimension |

`generateSNPs`

generates a matrix consisting of `n`

observations,
`snp.no=gene.no*block.no*block.size`

SNPs with genotypes coded by 0, 1 and 2, two automatically generated covariates for adjustment or matching and the matchset numbers. The neighborhood probabilities for SNPs is given by `p.different`

and/or `p.same`

and the allele frequencies for SNPs is given by `p.minor`

. The allele frequencies (`p.minor`

) and the probabilities for neighborhood blocks (`p.different`

) and/or `p.same`

, respectively, can differ between the blocks on a gene but are repeated similar over all genes `gene.no`

. The simulated SNP data structure is similar as in Schwender et al. (2011).

The response is determined by a logistic regression model given the SNPs, the binary covariate and the continuous covariate in the sim.cov matrix:

`P(Y=1|sim.cov)=exp(sim.cov*beta)/(1+exp(sim.cov*beta))`

Using the the model `P(Y=1|sim.cov)`

is computed for each subject in `n.sample`

, then the case and one control status for each of the `n.sample`

subjects are determined by drawn randomly from a Bernoulli distribution using the probability `P(Y=1|sim.cov)`

. From these `n.sample`

subjects one case and one control observation is randomly drawn. This algorithm is repeated `n/2`

times for each randomly sampled value from the continuous covariate, i.e. one case and one control is randomly drawn from each of `n/2`

times to generate the complete response vector of `length(n)`

.

As output `generateSNPs`

provides a response vector `y`

, a SNP matrix `x`

, a covariate matrix `cov`

and a matchset vector `matchset`

which can directly be used as input for the `minPtest`

, see the example of the `minPtest`

function.

An object of class 'generateSNPs', which is a list containing the following components:

`sim.data` |
a matrix with |

`y` |
a numeric response vector coded with 0 (coding for controls) and 1 (coding for cases) of length |

`x` |
a numeric |

`cov` |
a |

`matchset` |
a numeric vector of length |

`snp.no` |
number of SNPs in the simulated data set. |

`SNPtoGene` |
the mapping matrix of dimension |

`call` |
call. |

Stefanie Hieke hieke@imbi.uni-freiburg.de

Schwender, H. et al. (2011). Testing SNPs and sets of SNPs for importance in association studies. Biostatistics, 12, 18-32.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
# Generate a data set consisting of 100 subjects and 200 SNPs on 5 genes,
# with 4 blocks per gene with block size of 10, i.e. 10 SNPs per block
# yielding 40 SNPs per gene:
# specifying the matrix for 6 SNPs and corresponding parameters (effect size)
# for the generation of case-control status
SNP <- c(6,26,54,135,156,186)
BETA <- c(0.9,0.7,1.5,0.5,0.6,0.8)
SNPtoBETA <- matrix(c(SNP,BETA),ncol=2,nrow=6)
colnames(SNPtoBETA) <- c("SNP.item","SNP.beta")
set.seed(191)
sim1 <- generateSNPs(n=100,gene.no=5,block.no=4,block.size=10,p.same=0.9,
p.different=0.75,p.minor=c(0.1,0.4,0.1,0.4),n.sample=80,SNPtoBETA=SNPtoBETA)
# to reconstruct how to adopt the output from generateSNPs,
# see the example of the minPtest function.
``` |

```
Loading required package: scrime
Loading required package: Epi
Attaching package: 'Epi'
The following object is masked from 'package:base':
merge.data.frame
```

minPtest documentation built on May 29, 2017, 1:06 p.m.

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