MTaSPUsSetScore: gene-Multitrait Sum of Powered Score (MTSPUsSetScore) tests...

In ikwak2/aSPU: Adaptive Sum of Powered Score Test

Description

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

Usage

MTaSPUsSetScore(
  Zs,
  corSNP,
  corPhe,
  pow = c(1, 2, 4, 8),
  pow2 = c(1, 2, 4, 8),
  n.perm = 5000,
  Ps = FALSE
)

Arguments

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 MTSPUsSetScore test.
pow2	GENE specific power(gamma values) used in MTSPUsSetScore 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.

Value

A vector object, MTSPUsSet test, MTScore test P values and MTaSPUsSet_Score P value.

Author(s)

Il-Youp Kwak and Wei Pan

References

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

Examples

data(SAMD11)
attach(SAMD11)
## example analysis using aSPUM test.
(outFZ <- MTaSPUsSetScore(ZsF, corSNP=corSNPF, corPhe = corPheF,
      pow=c(1,2,4,8),  pow2 = c(1,2,4,8), n.perm=10, Ps=FALSE))

ikwak2/aSPU documentation built on July 2, 2021, 6:14 p.m.