gates {COMBAT}

Calling Gene-based Association Tests

Description

Several gene-based association tests methods are implemented.

Usage

gates(x, cor_G)
vegas(x, cor_G, vegas.pct=c(0.1,0.2,0.3,0.4,1), max.simulation=1e6)
simpleM(x, cor_G, pca_cut_perc=0.995)

Arguments

x

a vector of SNP-level P values.

cor_G

SNP-SNP correlation matrix.

vegas.pct

a numeric vector, specifying the fraction of the top SNPs to be used in the VEGAS method.

max.simulation

maximum number of simulations to be performed. Must be at least 1e6.

pca_cut_perc

cutoff for percentage of sum of eigen values.

Details

Function gates implements the GATES method (Li et al 2011, American Journal of Human Genetics 88:283-293), vegas implements VEGAS with different proportion tests (Liu et al 2010, American Journal of Human Genetics 87:139-145), and simpleM is the simpleM method (Gao et al 2008, Genetic Epidemiology 32:361-369).

Value

P value(s).

See Also

COMBAT, ld.Rsquare.

Examples

# read SNP P values
file1 <- paste(path.package("COMBAT"),"extdata","SNP_info.txt.gz",sep="/")
snp.info  <- read.table(file1, header = TRUE, as.is=TRUE)
snp.pvals <- as.matrix(snp.info[,2])

# read reference genotype
file2 <- paste(path.package("COMBAT"),"extdata","SNP_ref.txt.gz",sep="/")
snp.ref   <- read.table(file2, header = TRUE)
snp.ref   <- as.matrix(snp.ref)

#compute correlation among SNPs
cor_G <- ld.Rsquare(snp.ref)

#call gates
(pval_gates <- gates(x=snp.pvals, cor_G=cor_G))

#call vegas
(pval_vegas <- vegas(x=snp.pvals, cor_G=cor_G))

#call simpleM
(pval_simpleM <- simpleM(x=snp.pvals, cor_G=cor_G))