MTaSPUsSet {aSPU}

gene-Multitrait Sum of Powered Score (MTSPUsSet) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics.

Description

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

Usage

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

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 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.

Value

A vector object, MTSPUsSet test P values and MTaSPUsSet 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 MTaSPUsSet test.
(outFZ <- MTaSPUsSet(ZsF, corSNP=corSNPF, corPhe = corPheF,
      pow=c(1,2,4,8),  pow2 = c(1,2,4,8), n.perm=10, Ps=FALSE))