aSPU (version 1.36)

GatesSimes: GATES-Simes test for pathway-based association testing

Description

Get the p-value of GATES-Simes. It uses an extended Simes procedure to combine GATES p-values across multiple genes in a pathway.

Usage

GatesSimes(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.

References

Hongsheng Gui, Miaoxin Li, Pak C Sham and Stacey S Cherny (2011) Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease BMC Research Notes, 4:386

See Also

Hyst GATES2

Examples

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 <- GatesSimes(pvec = logitp, ldmatrix = ldmat, snp.info = simula$snp.info,
                  gene.info = simula$gene.info)
out