glossi {cpvSNP} | R Documentation

## 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.

### 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.

### 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.

### Author(s)

Jason Hackney, Jessica Larson, Caitlin McHugh mchughc@uw.edu

### 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)

[Package cpvSNP version 1.12.0 Index]