snps.assoc: The phenotypically-associated sites in the 'snps' matrix.
In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS
snps.assoc R Documentation
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 caitiecollins@gmail.com
caitiecollins/treeWAS documentation built on Feb. 11, 2025, 11:25 a.m.
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| snps.assoc | R Documentation |
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 caitiecollins@gmail.com
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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