AhRs: Sample data for partitionMetric

In partitionMetric: Compute a distance metric between two partitions of a set

Description

This small dataset contains aligned protein sequences for seven alleles of the aryl hydrocarbon receptor (AhR).

Usage

data(AhRs)

Format

The format is a character matrix in which column i represents the i'th position in the alignment, and contains an amino acid code or "-" indicating an indel. Row names contain the animal species.

Details

A DNA or protein sequence has an associated index set {1, 2, ..., n} that labels the n positions of the nucleotides or amino acids (AA). This index set can be partitioned such that all members referring to the same AA share a homogeneous partition. For example, given the sequence ATGTA and its index set {1,2,…,5}, the "A" partition contains the subset {1,5}, the "T" partition contains {2,4}, and so on.

Given two aligned sequences and their respective partitions of the index set, a metric distance between these partitions can be computed. See partitionMetric for such a metric, along with an example of clustering this AhR dataset.

Source

This dataset was derived from NCBI HomoloGene:1224.

References

Mark Hahn, Aryl hydrocarbon receptors: diversity and evolution. Chem Biol Interact, 2002, 141, 131-160

partitionMetric documentation built on May 2, 2019, 2:45 a.m.