vegas: Calculate the P-Value for a Set Using the VEGAS Method

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

Description

Calculates the p-value representing the association of the set with the phenotype of interest.

Usage

vegas(set, assoc_table, ldMatrix, num_sims = 1000, correction = TRUE,
  seed = NULL, verbose = FALSE)

Arguments

set	A GeneSet object containing a set of genes of interest or a GeneSetCollection object containing a collection of GeneSets.
assoc_table	An object of class GRanges. This object should at least contain columns SNP and P which hold SNP rsIDs and their corresponding association test p-values, respectively.
ldMatrix	A square, symmetric matrix of LD values, with each row and column corresponding to each of the items in the set. The diagonal entries should be 1, indicating the LD between an item in the set and itself is 1.
num_sims	A positive integer value for the number of simulations to be performed. Default is 1000.
correction	A logical argument indicating whether a value of one should be added to the numerator and denominator when calculating the p-value based upon the simulated statistics. By default, the correction is added and this argument is TRUE.
seed	An integer argument indicating what the random seed should be set to. This allows for replication of results. The default is NULL, and a random seed will be set internally.
verbose	A logical argument indicating whether output should be printed. The default is FALSE.

Details

This function calculates a p-value for sets of SNPs that reside within a gene set collection. We calculate the null distribution by taking into account the observed correlation among the SNPs and simulating a specified number of statistics from which the resulting p-value is calculated.

Value

An object with the corresponding VEGAS results. If set is a GeneSetCollection (i.e., multiple sets of interest), then the corresponding VEGASResultCollection is returned. If set is a GeneSet, a VEGASResult object will be returned.

Author(s)

Caitlin McHugh [e-mail]

References

Liu, Jimmy Z. and Mcrae, Allan F. et al. A Versatile Gene-Based Test for Genome-Wide Association Studies. The American Journal of Human Genetics, 2010.

cpvSNP documentation built on Nov. 8, 2020, 6 p.m.