Hyst: HYST (Hybrid Set-based Test) for single trait - pathway...
In ikwak2/aSPU: Adaptive Sum of Powered Score Test

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

Get a p-value using HYST.

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

`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.

A p-value.

Il-Youp Kwak and Wei Pan

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.

GatesSimes GATES2

#simula <- simPathAR1Snp(nGenes=20, nGenes1=1, nSNPlim=c(1, 20), nSNP0=1:3,
#                           LOR=.2, rholim=c(0,0),
#                           n=30, 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)