CNOGpro: Copy Numbers of Genes in prokaryotes
Version 1.1

Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms.

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AuthorOla Brynildsrud, Lars-Gustav Snipen
Date of publication2015-01-12 23:06:41
MaintainerOla Brynildsrud <ola.brynildsrud@nmbu.no>
LicenseGPL-2
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("CNOGpro")

Man pages

carsonella: CNV experiment of C. Carsonella ruddy (artificial data)
CNOGpro: Set up a new CNOGpro experiment
CNOGpro-internal: Internal CNOGpro Functions
CNOGpro-package: CNOGpro - Copy Numbers of Genes in Prokaryotes
normalizeGC: Normalization of read count data by GC content
plotCNOGpro: Plots the results of a 'CNOGpro' experiment
printCNOGpro: Prints the results of a 'CNOGpro' experiment
runBootstrap: Gene copy numbers with confidence intervals through...
runHMM: Copy number variation inference through a Hidden Markov Model
store: Store the results of a 'CNOGpro' copy number experiment
summaryCNOGpro: Summarize the 'CNOGpro' experiment

Functions

CNOGpro Man page Source code
CNOGpro-package Man page
HMMcopynumber Man page Source code
addState Man page Source code
calculateProb Man page Source code
carsonella Man page
copynumberBootstrap Man page Source code
getGCinwindows Man page Source code
getMembership Man page Source code
gethits Man page Source code
getreadcounts Man page Source code
getsequence Man page Source code
insertRow Man page Source code
isbetween Man page Source code
makeViterbimat Man page Source code
normalizeGC Man page Source code
plotCNOGpro Man page Source code
printCNOGpro Man page Source code
readGenBank Man page Source code
rgammapois Man page Source code
runBootstrap Man page Source code
runHMM Man page Source code
sampleChromosome Man page Source code
setupEmissionMatrix Man page Source code
setupTransitionMatrix Man page Source code
solvePR Man page Source code
spans Man page Source code
store Man page Source code
summaryCNOGpro Man page Source code
updateGeneTable Man page Source code

Files

inst
inst/extdata
inst/extdata/CP003467.gbk
inst/extdata/carsonellahits.tab
NAMESPACE
data
data/carsonella.rda
R
R/calculateProb.R
R/addState.R
R/CNOGpro.R
R/printCNOGpro.R
R/getsequence.R
R/updateGeneTable.R
R/gethits.R
R/runBootstrap.R
R/copynumberBootstrap.R
R/solvePR.R
R/setupEmissionMatrix.R
R/normalizeGC.R
R/CNOGpro-internal.R
R/store.R
R/makeViterbimat.R
R/getGCinwindows.R
R/setupTransitionMatrix.R
R/insertRow.R
R/readGenBank.R
R/getreadcounts.R
R/plotCNOGpro.R
R/getMembership.R
R/isbetween.R
R/summaryCNOGpro.R
R/rgammapois.R
R/spans.R
R/HMMcopynumber.R
R/sampleChromosome.R
R/runHMM.R
MD5
DESCRIPTION
man
man/runHMM.Rd
man/plotCNOGpro.Rd
man/normalizeGC.Rd
man/store.Rd
man/printCNOGpro.Rd
man/summaryCNOGpro.Rd
man/CNOGpro-package.Rd
man/runBootstrap.Rd
man/carsonella.Rd
man/CNOGpro.Rd
man/CNOGpro-internal.Rd
CNOGpro documentation built on May 19, 2017, 5:03 p.m.