aSPUsPath {aSPU}

Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics.

Description

It gives p-values of the SPUsPath tests and aSPUsPath test with GWAS summary statistics.

Usage

aSPUsPath(
  Zs,
  corSNP,
  pow = c(1, 2, 4, 8, Inf),
  pow2 = c(1, 2, 4, 8),
  snp.info,
  gene.info,
  n.perm = 1000,
  Ps = FALSE,
  prune = TRUE
)

Arguments

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

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.

prune

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

Value

P-values for SPUMpath tests and aSPUMpath test.

Author(s)

Il-Youp Kwak and Wei Pan

References

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

See Also

aSPUs

Examples

data(kegg9)

# p-values of SPUpath and aSPUpath tests.
out.a <- aSPUsPath(kegg9$nP, corSNP = kegg9$ldmatrix, pow=c(1:8, Inf),
                  pow2 = c(1,2,4,8), 
                  snp.info=kegg9$snp.info, gene.info = kegg9$gene.info,
                  n.perm=5, Ps = TRUE)

out.a