| AhRs {partitionMetric} | R Documentation |
Sample data for partitionMetric
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,\ldots,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,\ldots,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