vegas: Perform VEGAS Gene-Based Association Analysis
In psoerensen/qgg: Statistical Tools for Quantitative Genetic Analyses

vegas

R Documentation

Perform VEGAS Gene-Based Association Analysis

Description

This function performs VEGAS (Versatile Gene-based Association Study) to analyze gene-level associations using marker statistics and linkage disequilibrium (LD) structure from a reference panel.

Usage

vegas(
  Glist = NULL,
  sets = NULL,
  stat = NULL,
  p = NULL,
  threshold = 1e-10,
  tol = 1e-07,
  minsize = 2,
  verbose = FALSE
)

Arguments

`Glist`	A list containing genomic information, such as LD matrices or genotype data. Required.
`sets`	A list of sets (e.g., genes with their associated markers) to analyze. Required.
`stat`	A data frame containing marker-level statistics. Must include 'rsids' (marker IDs) and 'p' (p-values).
`p`	A numeric matrix of p-values for markers across multiple studies. If provided, 'stat' should be NULL.
`threshold`	A numeric value specifying the lower bound for p-values to avoid numerical issues. Default is '1e-10'.
`tol`	A numeric value specifying the tolerance for eigenvalues in LD matrices. Default is '1e-7'.
`minsize`	An integer specifying the minimum number of markers required for a set to be analyzed. Default is '2'.
`verbose`	A logical value indicating whether to print progress messages. Default is 'FALSE'.

Details

The function uses marker-level statistics to compute gene-level association statistics, accounting for LD structure among markers. The LD structure is retrieved from 'Glist', which should include precomputed LD matrices or genotype data for the markers.

Two modes are supported: - **'stat' Mode**: Uses marker statistics (e.g., p-values) from a single study to compute gene-level statistics. - **'p' Mode**: Uses marker p-values across multiple studies for meta-analysis of gene-level statistics.