Description Usage Arguments Details Value Author(s) References Examples

View source: R/pleio.q.sequential.R

Perform sequential tests of pleiotropy to determine the number of traits, and which traits, are associatd with a vector of genotypes. For gaussian traits without covariates.

1 | ```
pleio.q.sequential(obj.fit, pval.threshold)
``` |

`obj.fit` |
result of pleio.q.fit |

`pval.threshold` |
p-value for rejecting the null hypothesis of the specified number of non-zero betas. |

Perform sequential tests of pleiotropy, starting at the usual multivarite null hypothesis that all coefficients = 0. If this test rejects because the p-value < pval.threshold, then allow one coefficient to be non-zero in order to test whether the remaining coefficients = 0. If the test of one non-zero coefficient rejects, then allow two non-zero coefficients, considering all possible combinations of two non-zero coefficients and test whether the remaining coefficients = 0. Continue this sequential testing until the p-value for a test is greater than the specific pval.threshold. The step at which the p-value > pval.threshold determines which traits are associated with the genotype. If there are m traits, the sequential testing stops either when p-value > pval.threshold, or when (m-1) traits are tested. If the p-value remains less than pval.threshold when testing (m-1) traits, this implies that all m traits are associated with the genotype.

A list containing:

`pval ` |
p-value of the final test from the sequential testing |

`index.beta` |
index of columns of y that have non-zero betas. These indices indicate which traits are associated with the genotype, accounting for the correlations among the traits. |

Dan Schaid and Jason Sinnwell

Schaid DJ, Tong X, Larrabee B, Kennedy RB, Poland GA, Sinnwell JP. Statistical Methods for Testing Genetic Pleiotropy. To appear in Genetics, 2016.

1 2 3 4 | ```
data(pleio.qdemo)
fit <- pleio.q.fit(y, geno)
test.seq <- pleio.q.sequential(fit, pval.threshold=.05)
test.seq
``` |

pleio documentation built on Dec. 7, 2018, 1:05 a.m.

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.