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.
