Hyst: HYST (Hybrid Set-based Test) for single trait - pathway...

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

Description

Get a p-value using HYST.

Usage

1
Hyst(pvec, ldmatrix, snp.info, gene.info)

Arguments

pvec

p-values for each SNP.

ldmatrix

numeric. A correlation matrix of SNPs with dimensions matching the length of pvec (the number of SNPs).

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.

Value

A p-value.

Author(s)

Il-Youp Kwak and Wei Pan

References

Miao-Xin Li, Johnny S.H. Kwan and Pak C. Sham (2012) HYST: A Hybrid Set-Based Test for Genome-wide Association Studies, with Application to Protein-Protein Interaction-Based Association Analysis The American Journal of Human Genetics, 91, 478-488.

See Also

GatesSimes GATES2

Examples

1
2
3
4
5
6
7
8
9
simula <- simPathAR1Snp(nGenes=20, nGenes1=1, nSNPlim=c(1, 20), nSNP0=1:3,
                           LOR=.2, rholim=c(0,0),
                           n=100, MAFlim=c(0.05, 0.4), p0=0.05)
logitp <- getlogitp(simula$Y, simula$X)

## get correlation of SNPs using controls
ldmat <- cor(simula$X[ simula$Y == 0, ])
out <- Hyst(pvec = logitp, ldmatrix = ldmat, snp.info = simula$snp.info,
            gene.info = simula$gene.info)

aSPU documentation built on May 1, 2019, 7:04 p.m.