Description Usage Arguments Value Author(s) References Examples

`aSPU_perm`

returns p-values of the SPU tests and aSPU test.

1 2 |

`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). |

`resample` |
Resample methods. "perm" for residual permutations; "boot" for parametric bootstrap. |

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

`pow` |
Gamma set used in SPU test. A vector of the powers. |

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

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

Wei Pan, Junghi Kim, Yiwei Zhang, Xiaotong Shen and Peng Wei (2014) A powerful and adaptive association test for rare variants, Genetics, 197(4), 1081-95

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
p = 200
n = 100
beta = c(1,3,3)
s = 0.15
signal.r = 0.08
non.zero = floor(p * s)
seed = 2
alpha = c(rep(signal.r,non.zero),rep(0,p-non.zero))
dat = generate_data(seed, n = n, p = p, beta = beta,alpha = alpha)
cov = dat$Z
X = dat$X
Y = dat$Y
aSPU_perm(Y, X, cov = cov, pow = c(1:6, Inf),resample = "perm", model = "gaussian", n.perm = 1000)
# The p-values are similar to the asymptotic based one
``` |

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