Description Usage Arguments Details Value Author(s) References Examples

`Goeman_perm`

returns resample based p-value for a test proposed by Goeman (2011).

1 2 | ```
Goeman_perm(Y, X, cov = NULL, model = c("gaussian", "binomial"),
n.perm = 1000)
``` |

`Y` |
Response. It can be binary or continuous trait. A vector with length n (number of observations). |

`X` |
Genotype or other data; each row for a subject, and each column for a variable of interest. An n by p matrix (n: number of observations, p: number of predictors). |

`cov` |
Covariates. An n by q matrix (n: number of observations, q: number of covariates). |

`model` |
corresponding to the Response. "gaussian" for a quantitative response; "binomial" for a binary response. |

`n.perm` |
number of permutations or bootstraps. |

`Goeman_perm`

calculates the resample based p-value. You can calculate the asymptotic based p-value via using R package globaltest. Based on our experience, resample based p-value is often different from the asymptotic based one, except when the dimension of X is larger than the sample size n.

A list object, Ts : test statistics for the SPU tests and the aSPU test. pvs : p-values for the SPU and aSPU tests.

Chong Wu and Wei Pan

Goeman, J. J., Van Houwelingen, H. C. and Finos, L. (2011). Testing against a high-dimensional alternative in the generalized linear model asymptotic type 1 error control. Biometrika, 98(2), 381-390.

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