COMBAT (version 0.0.2)

COMBAT: A Combined Gene-based Association Test

Description

This function implements a combined gene-based association test using SNP-level P valuese and reference genotype data.

Usage

COMBAT(x, snp.ref, vegas.pct = c(0.1,0.2,1), nperm = 75,
   seed=12345, ncores=1)

Arguments

x

a vector of SNP-level P values.

snp.ref

a matrix of SNP genotypes (coded as allele counts) from reference samples, with samples in rows and SNPs in columns.

vegas.pct

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

nperm

number of permutations for computing the correlation between P values of different tests.

seed

random seed to derive consistent outcome.

ncores

number of CPU cores for parallel computing.

Value

A vector of p-values from differrnt gene-based tests with summary statistics. By default, 7 tests will be computed: GATES, 4 VEGAS tests, SimpleM and one COMBAT.

Details

Some technical details about the method.

References

Jianfei Huang, Minghui Wang, James B. Potash, Shizhong Han. COMBAT: A Combined Association Test for Genes using Summary Statistics. Manuscript submitted.

See Also

ext_simes, gates, vegas.

Examples

# NOT RUN {
# 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)

#call COMBAT; not run
#COMBAT(snp.pvals, snp.ref, nperm=50)

# }