carsonella: CNV experiment of C. Carsonella ruddy (artificial data)

In CNOGpro: Copy Numbers of Genes in prokaryotes

Description

This is an example object of class CNOGpro, as created by the CNOGpro method. The input to this file was a GenBank flat file (Acc. nr: CP003467), and a table of best-hit read locations from a resequencing experiment. The data were created by artificially duplicating one gene and removing another from the chromosome, and is meant for illustration purposes only. The reads were created by the ART sequencing simulator by Huang et al. (2011)

Usage

data(carsonella)

Format

An object of class CNOGpro

Source

Artificial data, produced by the author

References

Huang,W. et al. (2011) ART: a next-generation sequencing read simulator. Bioinformatics, 28, 593–594.
Nakabachi,A. et al. (2013) Defensive bacteriome symbiont with a drastically reduced genome. Curr. Biol., 23, 1478 – 1484

Examples

data(carsonella)
summaryCNOGpro(carsonella)
plotCNOGpro(carsonella)

Example output

Loading required package: seqinr
CNOGpro copy number analysis experiment of C. Carsonella ruddii, artificial example data 
Windowlength: 100 

Summary statistics of chromosome: CP003467 
Length:  174014 	Number of genetic elements:  303 	Mean coverage:  66.5375 	Variance:  132.5474 
Data not yet normalized

CNOGpro documentation built on May 2, 2019, 5:57 a.m.