get_GxE: Get data frames of types of GxE from a mash object

In Alice-MacQueen/snpdiver: Explore SNP Effects on Multiple Phenotypes in Diversity Panels

Description

Performs set operations to determine pairwise GxE for effects from a mash object.

Usage

get_GxE(m, factor = 0.4, thr.m = 0.05, thr.r2 = NA)

Arguments

m	An object of type mash
factor	a number between 0 and 1. The factor within which effects are considered to be shared.
thr.m	Numeric. The threshold for including an effect in the assessment in mash. Default is 0.05.
thr.r2	Numeric. Value between 0 and 1. The r^2 value above which effects are considered to be linked; in this case, only the SNP with the more significant log10Bayes Factor value in mash is kept.

Value

A list containing eight data frames. Those with names that start "S_" contain significant effects of different types between pairs of named rows and columns. S_all_pairwise contains all significant effects; NS_pairwise contains all non-significant effects. S_CN contains effects significant in only one condition, and effects with a significantly different magnitude (differential sensitivity). This dataframe is not conservative using the local false sign rate test - we can't determine the sign of one of the effects for effects significant in only one condition - so it's not recommended to use this, but included. S_2_no contains effects significant in both conditions that do not differ significantly in magnitude. These effects do not have GxE. S_AP contains effects significant in both conditions that differ in their sign - and have antagonistic pleiotropy. S_DS contains effects significant in both conditions that differ in the magnitude of their effect, but not their sign - differentially sensitive alleles. S_1_row and S_1_col contain effects that are significant in just one of the two conditions - the row or the column, respectively.

Alice-MacQueen/snpdiver documentation built on Dec. 17, 2021, 8:41 a.m.