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

Computes the original and permuted values of the test statistic of the gTDT test as proposed by Cordell (2002) for each interaction between the pairs of SNPs in mat.snp.

1 2 |

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

`n.perm` |
number of permutations of the response for which the permuted values of the test statistic should be computed. |

`genes` |
a character vector containing the names of the genes to which the SNPs belong. If specified, only the two-way interactions
between SNPs from different genes are tested. If |

`col.out` |
the output of |

`warnError` |
logical indicating whether the statistics for the gTDT should be returned as |

`verbose` |
logical indicating whether some information on what is currently computed should be printed. |

`rand` |
numeric value. If specified, the random number generator is set into a reproducible state. |

A list consisting of

`stat` |
a numeric vector containing the original values of the test statistic, |

`permStat` |
a numeric matrix containing the permuted values of the test statistic, |

`y.perm` |
a matrix containing the permutations of the response. |

Holger Schwender, holger.schwender@udo.edu

Cordell, H. J. (2002). Epistasis: What it Means, what it Doesn't mean, and Statistical Methods to Detect it in Humans. Human Molecular Genetics, 11, 2463-2468.

1 2 3 4 5 6 7 8 9 10 11 | ```
# Load the simulated data.
data(trio.data)
# Cordell's LRT for all pairs of SNPs in mat.test can be performed
# and the values of the LRT statistic for 10 permutations of the
# case-pseudo-controls status can be computed by
gxg <- colGxGPerms(mat.test, n.perm = 10)
# where we here consider only 10 permutations to keep the computing
# time of this example small. Usually, at least a few thousand
# permutations should be considered.
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.