genotype.saap.msa


The genotype.saap.msa data is a multiple sequence alignment in Biostrings
AAMultipleAlignment format. It contains 120 protein sequences, each with 154
sites (SAAPs). 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.msa function

AAMultipleAlignment object with 120 sequences each made of 154 amino acid
sites (SNPs), some of which qualify as single amino acid polymorphisms.

Format

Source

The genotype.saap.msa data is a multiple sequence alignment in Biostrings
AAMultipleAlignment format. It contains 120 protein sequences, each with 154
sites (SAAPs). 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.msa: SAAP genotype dataset (msa)

Description

Usage

Arguments

Value

Format

Source

Examples