snps.assoc: The phenotypically-associated sites in the 'snps' matrix.

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

The phenotypically-associated sites in the snps matrix.

Description

This vector specifies the identities (names) of the loci in the genetic data matrix (see: data(snps)) that have been simulated along the phylogenetic tree (see: data(tree)) to be in statistical association with the phenotype (see: data(phen)). Comparing this vector of snps column names to the set of snps loci identified by treeWAS allows us to evaluate the performance of the treeWAS GWAS method. After applying treeWAS to the components of this dataset, using: treeWAS(snps, phen, tree), we can assess the ability of treeWAS to recover these "known" associated sites via any of its three association scores (see the treeWAS vignette).

Usage

data(snps.assoc)

Format

A vector of length 10.

Author(s)

Caitlin Collins [e-mail]

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