cpvSNP (version 1.4.0)

glossi: Calculate a Chi-squared Statistic and P-Value for Independent Items of a Set Using the GLOSSI Method

Description

Calculates the p-value representing the association of the set with the phenotype of interest, assuming all items in the set are independent, using the GLOSSI method.

Usage

glossi(pvals, snp.gsc)

Arguments

pvals

A numerical vector of p-values with names corresponding to elements listed in the geneIds slot in the snp.gsc object.

snp.gsc

An object of class GeneSetCollection where geneIds holds the items of each set corresponding to the pvals.

Value

An object with the corresponding GLOSSI results. If snp.gsc is a GeneSetCollection (i.e., multiple sets of interest), then the corresponding GLOSSIResultCollection is returned. If snp.gsc is a GeneSet, a GLOSSIResult object will be returned.

Details

This function calculates a p-value for sets of SNPs that reside within a gene set collection. We calculate the chi- square p-values and statistic by applying Fisher's transformation to the observed p-values.

References

Chai, High-Seng and Sicotte, Hughes et al. GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. BMC Bioinformatics, 2009.

Examples

    set.seed(30)
    pvals <- runif(100)
    names(pvals) <- paste0("rs", 1:100)
    snpGS5 <- GeneSet(geneIds=names(pvals)[1:5], setName="set5")
    res <- glossi (pvals, snpGS5)