ebola: Ebolavirus genome sequence data

In EnsCat: Clustering of Categorical Data

Description

A dataset consisting of whole genome sequences for Ebolavirus from the family Filovirdae.

Usage

data("ebola")

Format

The format of the data is a list with components $obs and $lab. "ebola$obs" includes the observations that are stored as numerical values. "ebola$lab" contains the labels of the data.

This ebola$obs is a matrix of dimension 103x26445 that represents the sequences of 103 viral genomes from the Ebolavirus.

Details

This data includes whole genome sequences of viruses belonging to the Ebolavirus. Ebolavirus is a subfamily of the Filovirdae family of viruses. The data is downloaded from ViPR, http://www.viprbrc.org, and are aligned using "MAFFT", see Katoh et a. (2013), and saved in "ebola". Ebolavirus subdivides into five species: Bundibugyo virus (Bun), Reston ebolavirus (Res), Sudan ebolavirus (Sud), Tai Forest ebolavirus (Tai), and Zaire ebolavirus (Zai). The hosts are human, monkey, swine, guinea pig, mouse, and bat (denoted hum, mon, swi, gpi, mou, bat, respectively, in our dataset). The ebola$lab in the example show the labels, the combination of species and host.

References

Katoh, K., and D.M. Standley (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4), 772-780.

Pickett, BE et al. (2012). ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Research 40: D593-8.

Examples

### load Ebolavirus data
#data("ebola")

EnsCat documentation built on May 1, 2019, 8:45 p.m.