genotype.saap


The genotype.saap data is a character matrix with dimensions 120x154.
It contains 154 amino acid protein sites across 120 organisms. The data
is used in combination with the phenotype.aa data to quantify the
association between each amino acid substitution pair and the phenotype
vector.


Given a set of genetic polymorphisms in the form of single
nucleotide poylmorphisms or single amino acid polymorphisms and
a corresponding phenotype data, often we are interested to
quantify their association such that we can identify the causal
polymorphisms. Using statistical learning techniques such as
random forests and support vector machines, this tool provides
the means to estimate genotype-phenotype associations. It also
provides visualization functions which enable the user to
visually inspect the results of such genetic association study
and conveniently select the genotypes which have the highest
strenght ofassociation with the phenotype.

Simo Kitanovski

genphen

A tool for computing genotype-phenotype associations using
statistical learning techniques

genotype.saap function

A matrix with 120 observations and 154 columns (some of which qualify
as single amino acid polymorphisms).

Format

Source

The genotype.saap data is a character matrix with dimensions 120x154.
It contains 154 amino acid protein sites across 120 organisms. The data
is used in combination with the phenotype.aa data to quantify the
association between each amino acid substitution pair and the phenotype
vector.

genotype.saap: SAAP genotype dataset

Description

Usage

Arguments

Value

Format

Source

Examples