vegasMarginal: 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

vegasMarginal(pvals, ld_matrix, num_sims, correction = TRUE, seed = NULL,
  verbose = FALSE)

Arguments

pvals	A vector of p-values corresponding to items in the set.
ld_matrix	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	An integer value for the number of simulations to be performed.
correction	A logical argument indicating whether a value of one should be added to the numerator when calculating the p-value based upon the simulated statistics. By default, the correction is added. An argument of FALSE will not add one to the numerator.
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 periodic output should be printed. Defaults to FALSE, indicating no output will be printed.

Details

This is a helper function to calculate the p-value for a set of SNPs that reside within a gene set collection. The correlation among the SNPs is taken into account by the LD matrix. The resulting p-value is calculated from a null distribution that is simulated num_sims times based upon the specified correlation structure.

Value

A VEGASResult object with the corresponding VEGAS results.

Author(s)

Caitlin McHugh [e-mail]

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