aSPU (version 1.36)

aSPUMpath: Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for meta-analyzed data.

Description

It gives p-values of the SPUpath tests and aSPUpath test for meta-analyzed data.

Usage

aSPUMpath(Zs, corrSNP, pow = c(1, 2, 4, 8, Inf), pow2 = c(1, 2, 4, 8),
  snp.info, gene.info, n.perm = 1000, Ps = FALSE)

Arguments

Zs

Z-scores for each SNPs. It could be P-values if the Ps option is TRUE.

corrSNP

Correaltion matirx of SNPs. Estimated from the reference population.

pow

SNP specific power(gamma values) used in SPUpath test.

pow2

GENE specific power(gamma values) used in SPUpath test.

snp.info

SNP information matrix, the 1st column is SNP id, 2nd column is chromosome #, 3rd column indicates SNP location.

gene.info

GENE information matrix, The 1st column is GENE id, 2nd column is chromosome #, 3rd and 4th column indicate start and end positions of the gene.

n.perm

number of permutations.

Ps

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

Value

• P-values for SPUMpath tests and aSPUMpath test.

References

Wei Pan, Il-Youp Kwak and Peng Wei (2015) A Powerful and Pathway-Based Adaptive Test for Genetic Association With Common or Rare Variants (Submitted)

See Also

simPathAR1Snp aSPUpathSingle aSPUpath

Examples

data(kegg9)

# p-values of SPUpath and aSPUpath tests.
out.a <- aSPUMpath(kegg9$nZ, corrSNP = kegg9$ldmatrix, pow=c(1:8, Inf),
                  pow2 = c(1,2,4,8),
                  snp.info=kegg9$snp.info, gene.info = kegg9$gene.info,
                  n.perm=10, Ps = TRUE)
out.a