set_p_test: Set the number of markers used in a GRM

In deruncie/GridLMM: Efficient Mixed Models for GWAS with multiple Random Effects

Set the number of markers used in a GRM

Description

For GRMs created as X'X, it can be useful to remove "proximal" markers from the GRM when testing a focal marker. To do this in GridLMM, we need to know p (how many markers were in the original GRM), and p_test, how many markers are to be removed for a typical test

Usage

set_p_test(V_setup, p_test = NULL, p = NULL)

Arguments

V_setup	A list of setup variables, as returned by a GridLMM function
p_test	A named vector with names corresponding to random effects in the model (as found in V_setup$RE_setup), and values equal to the typical number of markers to be removed for a typical test
p	A named vector as for p_test giving the total number of markers used to create the original GRM

Value

The modified V_setup list

deruncie/GridLMM documentation built on May 2, 2023, 7:18 p.m.