geneSetAnalysis

A list including the following components:	<code>arrayData</code> -- a data.frame of dimension 119487 rows and 4 columns including P-values, SNP ids, position and chromosome for a GWAS experiment;	<code>geneSets</code> -- a GeneSetCollection containing gene Entrez ids;	<code>ldMat</code> -- a matrix of dimension 871 x 871 holding linkage disequilibrium values;	<code>indepSNPs</code> -- a list containing 302 independent SNP ids;

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

geneSetAnalysis function

A list including the following components:

	<code>arrayData</code> -- a data.frame of dimension 119487 rows and 4 columns including P-values, SNP ids, position and chromosome for a GWAS experiment;

	<code>geneSets</code> -- a GeneSetCollection containing gene Entrez ids;

	<code>ldMat</code> -- a matrix of dimension 871 x 871 holding linkage disequilibrium values;

	<code>indepSNPs</code> -- a list containing 302 independent SNP ids;

geneSetAnalysis: Data to run gene set analysis methods

Description

Usage

Arguments

Examples