Description Usage Arguments Value Author(s) References Examples

It gives p-values of the MTSPUsSet tests and MTaSPUsSet test with GWAS summary statistics.

1 2 | ```
MTaSPUsSet(Zs, corSNP, corPhe, pow = c(1, 2, 4, 8), pow2 = c(1, 2, 4, 8),
n.perm = 5000, Ps = FALSE, prune = TRUE)
``` |

`Zs` |
Z-score matrix. row represent SNPs and column represent traits. It could be P-values if the Ps option is TRUE. |

`corSNP` |
Correlation matirx of the SNPs to be tested; estimated from a reference panel (based on the same set of the reference alleles as used in calculating Z-scores). |

`corPhe` |
Correlation matirx of phenotypes to be tested; Estimated from Z-scores. |

`pow` |
SNP specific power(gamma values) used in MTSPUsSet test. |

`pow2` |
GENE specific power(gamma values) used in MTSPUsSet test. |

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

`Ps` |
TRUE if input is p-value, FALSE if input is Z-scores. The default is FALSE. |

`prune` |
if it is TRUE, do pruing before the test using pruneSNP function. |

A vector object, MTSPUsSet test P values and MTaSPUsSet P value.

Il-Youp Kwak and Wei Pan

Il-Youp Kwak, Wei Pan (2017) Gene- and pathway-based association tests for multiple traits with GWAS summary statistics, Bioinformatics, 33(1), 64-71.

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