geneSets


	This gene set collection object provides four gene sets of varying sizes to be used as examples of how to run the <code>cpvSNP</code> package functions.


datasets

Gene set analysis methods exist to combine SNP-level
association p-values into gene sets, calculating a single
association p-value for each gene set. This package implements
two such methods that require only the calculated SNP p-values,
the gene set(s) of interest, and a correlation matrix (if
desired). One method (GLOSSI) requires independent SNPs and the
other (VEGAS) can take into account correlation (LD) among the
SNPs. Built-in plotting functions are available to help users
visualize results.

Caitlin McHugh

cpvSNP

Gene set analysis methods for SNP association p-values that lie
in genes in given gene sets

geneSets function

A <code>GeneSetCollection</code> object of length 4. The values stored in the <code>geneIds</code> slot are Entrez ids. Gene sets 1-3 were randomly selected with sizes 100, 200 and 50, respectively. The fourth GeneSet holds genes in which the simulated p-values for corresponding SNPs are significant.

Format

This gene set collection object provides four gene sets of varying sizes to be used as examples of how to run the <code>cpvSNP</code> package functions.

geneSets: Gene Set Collection object

Description

Usage

Arguments

Format