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

It gives p-values of the SPUs tests and aSPUs test with GWAS summary statistics.

1 2 |

`Zs` |
Z-scores for each SNPs. 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). |

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

`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 list object, Ts : test statistics for the SPU tests (in the order of the specified pow) and finally for the aSPU test. pvs : p-values for the SPUs and aSPUs tests.

Il-Youp Kwak and Wei Pan

Il-Youp Kwak, Wei Pan (2015) Adaptive Gene- and Pathway-Trait Association Testing with GWAS Summary Statistics, Bioinformatics, 32(8), 1178-1184.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ```
data(kegg9)
## example analysis using aSPUM test.
g <- kegg9$gene.info[1,1] # SOAT1
## Take snps mapped on gene "SOAT1" from the information of gene.info and snp.info.
snps <- which( ( kegg9$snp.info[,2] == kegg9$gene.info[kegg9$gene.info[,1] == g, 2] ) &
(kegg9$snp.info[,3] > kegg9$gene.info[kegg9$gene.info[,1] == g, 3] ) &
(kegg9$snp.info[,3] < kegg9$gene.info[kegg9$gene.info[,1] == g, 4] ) )
## Take subsets
newP <- kegg9$nP[snps] ;
ldsub <- kegg9$ldmatrix[snps, snps];
## Get p-value for gene SOAT1. Read vignette for details.
out <- aSPUs(newP, corSNP=ldsub , pow=c(1:8, Inf), n.perm=100, Ps=TRUE)
out$Ts
# This is a vector of Test Statistics for SPUM and aSPUM tests.
# SPUs1 to SPUsInf corresponds with the option pow=c(1:8, Inf)
# They are SPUs test statistics.
# The last element aSPUs is minimum of them, aSPUs statistic.
out$pvs
# This is a vector of p-values for SPUs and aSPUs tests.
# SPUs1 to SPUsInf corresponds with the option pow=c(1:8, Inf)
# They are p-values for corresponding SPUs tests.
# The last element is p-value of aSPUs test.
``` |

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