COMBAT (version 0.0.2)

ext_simes: Calling Gene-based Association Tests

Description

Calling Gene-based Association Tests.

Usage

ext_simes(x, cor_r)
gates(x, cor_G)
vegas(x, cor_G, vegas_vec, n_simul)

Arguments

x

a vector of SNP-level P values.

cor_r

correlation among P values.

cor_G

SNP-SNP correlation matrix.

vegas_vec

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

n_simul

number of simulations.

Value

P value(s).

Details

Function ext_simes implements extended Simes method, gates implements the GATES method, and vegas implements VEGAS with different proportion tests.

References

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

See Also

COMBAT

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)

# }

Run the code above in your browser using DataCamp Workspace