genotype.snp


The genotype.snp data is a character matrix with dimensions 51x100.
It contains 100 SNPs across 51 mouse strains, taken from the publicly
available Mouse Hapmap data. We used it in combination with the
phenotype.snp data to compute the association between each SNP and
the phenotype data.


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.snp function

A matrix with 51 observations (laboratory mouse strains) and 100
variables (SNPs).

Format

http://mouse.cs.ucla.edu/mousehapmap/emma.html

Source

The genotype.snp data is a character matrix with dimensions 51x100.
It contains 100 SNPs across 51 mouse strains, taken from the publicly
available Mouse Hapmap data. We used it in combination with the
phenotype.snp data to compute the association between each SNP and
the phenotype data.

genotype.snp: SNP genotype dataset

Description

Usage

Arguments

Value

Format

Source

Examples