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

Computes the test statistics and the corresponding p-values either for the Parent-of-Origin Likelihood Ratio Test proposed by Weinberg (1999) or the Transmission Asymmetry Test proposed by Weinberg et al. (1998).

1 2 3 4 5 6 7 8 9 |

`mat.snp` |
a numeric matrix in which each column represents a SNP. Each column must be
a numeric vector of length |

`size` |
the number of SNPs considered simultaneously when computing the test statistics. |

`stratified` |
should also test statistics and p-values stratified by paternal and maternal transmission be computed? |

`bothHet` |
a numeric value between 0 and 1 specifying how trios in which both parents are heterozygous are weighted in
determination of the TAT statistic. By default, such trios are ignored (as proposed by Weinberg, 1999). If |

`x` |
an object of class |

`digits` |
number of digits that should be printed. |

`top` |
number of interactions that should be printed. If |

`...` |
ignored. |

For `colPOlrt`

, an object of class `polrt`

consisting of the following numeric vectors:

`stat` |
the values of the test statistic of the likelihood ratio test for all SNPs in |

`pval` |
the corresponding p-values, |

`full` |
the values of the maximized likelihoods of the full models containing also a parameter for the parent-of-origin effect, |

`red` |
the values of the maximied likelihoods of the reduced models not containing this parameter. |

For `colTAT`

, an object of class `tat`

consisting of the following numeric vectors:

`stat` |
the values of the test statistic of transmission asymmetry test for all SNPs in |

`pval` |
the corresponding p-values, |

`usedTrios` |
the number of trios affecting the determination of the TAT statistic, |

and if `stratified = TRUE`

`matStrat` |
a matrix with four columns containing the number of minor alleles transmitted and not-transmitted by heterozygous fathers and mothers, |

`statPaternal` |
a numeric vector containing for each SNP the value of the test statistic for testing whether the numbers of paternal transmissions and non-transmissions differ, |

`pvalPaternal` |
the p-values corresponding to |

`statMaternal` |
a numeric vector containing for each SNP the value of the test statistic for testing whether the numbers of maternal transmissions and non-transmissions differ, |

`pvalMaternal` |
the p-values corresponding to |

Holger Schwender, holger.schwender@udo.edu

Weinberg, C.R.,Wilcox, A.J., and Lie, R.T. (1998). A Log-Linear Approach to Case-Parent-??Triad Data:
Assessing Effects of Disease Genes that act Either Directly or Through Maternal Effects and that
may be Subject to Parental Imprinting. *American Journal of Human Genetics*, 62, 969-978.

Weinberg, C.R. (1999). Methods for Detection of Parent-of-Origin Effects in Genetic Studies of
Case-Parents Triads. *American Journal of Human Genetics*, 65, 229-235.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
# Load the simulated data.
data(trio.data)
# The Parent-of-Origin Likelihood Ratio Test can be applied
# to the SNPs in mat.test by
po.out <- colPOlrt(mat.test)
# The Transmission Asymmetry Test can be applid to the SNPs
# in mat.test by
tat.out <- colTAT(mat.test)
# By default, statistics for the top 5 SNPs are displayed.
# If another number of SNPs, say 10, should be displayed,
# then this can be done by
print(po.out, top = 10)
# The statistics for all SNPs (not ordered by their
# significance) can be obtained by
print(po.out, top = 0)
``` |

```
Parent-Of-Origin Likelihood Ratio Test
LL (with) LL (without) Statistic P-Value
SNP1 -43.58 -44.19 1.2163 0.2701
SNP2 -38.55 -38.64 0.1882 0.6645
SNP3 -37.39 -37.93 1.0728 0.3003
SNP4 -37.92 -38.15 0.4693 0.4933
SNP5 -40.22 -40.49 0.5477 0.4593
SNP6 -40.57 -40.63 0.1222 0.7267
Parent-Of-Origin Likelihood Ratio Test
LL (with) LL (without) Statistic P-Value
SNP1 -43.58 -44.19 1.2163 0.2701
SNP2 -38.55 -38.64 0.1882 0.6645
SNP3 -37.39 -37.93 1.0728 0.3003
SNP4 -37.92 -38.15 0.4693 0.4933
SNP5 -40.22 -40.49 0.5477 0.4593
SNP6 -40.57 -40.63 0.1222 0.7267
```

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