plotCNOGpro: Plots the results of a 'CNOGpro' experiment

In CNOGpro: Copy Numbers of Genes in prokaryotes

Description

Plots the coverage in a number of ways: Coverage along the chromosome, density plots of coverage for each individual copy number state (as assigned by the runHMMmethod) and coverage by GC percentage of the reads, before and after normalization.

Usage

plotCNOGpro(experiment)

Arguments

experiment

An object of class CNOGpro

Author(s)

Ola Brynildsrud

See Also

CNOGpro

Examples

data(carsonella)
carsonella_normalized <- normalizeGC(carsonella)
carsonella_hmm <- runHMM(carsonella_normalized, nstates=5)
plotCNOGpro(carsonella_hmm)

Example output

Loading required package: seqinr
Normalizing read counts for GC bias...
Overall values for chromosome  CP003467 :
Median read count:  66 
Median GC percentage:  0.17 
Calculating per-read weight based on GC percentage...
Successfully normalized chromosome  CP003467 
Running HMM... 
Analyzing chromosome CP003467 
Finished setting up transition and emission matrices. Starting Viterbi algorithm...
Attempting to create Viterbi matrix
Positions 1 - 18800 : Most probable state =  1 
Positions 18801 - 22000 : Most probable state =  2 
Positions 22001 - 94200 : Most probable state =  1 
Positions 94201 - 95200 : Most probable state =  0 
Positions 95201 - 174014 : Most probable state =  1 
Finished running Viterbi algorithm. Assigning most probable states to individual segments...
Copy number analysis complete. Use print to access results.

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