simultaneous.test.epi: Test for association between genetic loci with Score 2.

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Test for association between genetic loci with Score 2.

Description

[*A work in progress; not curently integrated into treeWAS:*] Use the simultaneous.test (Score 2) to test for associations between genetic loci, which may indicate an epistatic interaction. This function can be used either to test for pairwise association between all pairs of genetic loci or for associations between a subset of snps and all other snps (recommended for large datasets; see details).

Usage

simultaneous.test.epi(snps.reconstruction, tree, snps.subset = NULL)

Arguments

snps.reconstruction	A matrix containing the terminal and reconstructed ancestral states of SNPs for all nodes in the tree.
tree	A phylo object containing the tree representing the ancestral relationships between the individuals for which snps and phen are known.
snps.subset	An optional vector (see details); else, NULL. The snps.subset vector can be a character vector, containing a subset of colnames(snps.rec), a logical vector, using TRUE or FALSE to indicate which columns are to be retained and excluded, or an integer vector, specifying the column indices to be retained.

Details

The number of pairwise tests between all pairs of snps grows rapidly as the number of snps columns increases. As such, for datasets where ncol(snps.reconstruction) is large, we recommend that the snps.subset argument is used to reduce the number of tests, by indicating which snps to test for association with all other snps. The snps.subset index can be used to select any subset of snps of interest. For example, one may wish to test for interactions between all snps and a subset of snps that had been deemed significantly associated with a particular phenotype in a previous run of treeWAS.

Author(s)

Caitlin Collins [e-mail]

caitiecollins/treeWAS documentation built on March 9, 2024, 3:15 p.m.