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.
vegas(
Glist = NULL,
sets = NULL,
stat = NULL,
p = NULL,
threshold = 1e-10,
tol = 1e-07,
minsize = 2,
verbose = FALSE
)A data frame with the results
A list containing genomic information, such as LD matrices or genotype data. Required.
A list of sets (e.g., genes with their associated markers) to analyze. Required.
A data frame containing marker-level statistics. Must include `rsids` (marker IDs) and `p` (p-values).
A numeric matrix of p-values for markers across multiple studies. If provided, `stat` should be NULL.
A numeric value specifying the lower bound for p-values to avoid numerical issues. Default is `1e-10`.
A numeric value specifying the tolerance for eigenvalues in LD matrices. Default is `1e-7`.
An integer specifying the minimum number of markers required for a set to be analyzed. Default is `2`.
A logical value indicating whether to print progress messages. Default is `FALSE`.
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.