Rnits: R Normalization and Inference of Time Series data
Version 1.10.0

R/Bioconductor package for normalization, curve registration and inference in time course gene expression data

AuthorDipen P. Sangurdekar <dipen.sangurdekar@gmail.com>
Bioconductor views DifferentialExpression GeneExpression Microarray Normalization TimeCourse
Date of publicationNone
MaintainerDipen P. Sangurdekar <dipen.sangurdekar@gmail.com>
LicenseGPL-3
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rnits")

Getting started

README.md

Popular man pages

fit-methods: Fit model on time series data
getLR-methods: Get log-ratios
getNormTwoChannel-methods: Get Normalized channel data for two channel arrays
rnits: rnits.
summarizeProbes-methods: Summarize probe level data to gene level data
timeAlign-methods: Curve registration of time series curves
topData-methods: Data of top genes/probes
See all...

All man pages Function index File listing

Man pages

build.Rnits: Input the RGlist raw data, build a Rnits object and perform...
calculateGCV-methods: Calculate the optimal B-spline model using generalized...
extract-methods: replace slot of Rnits
fit-methods: Fit model on time series data
getCID-methods: Cluster IDs of probes/genes from fitted 'Rnits'
getFitModel-methods: Extract fit data from 'Rnits' object
getLR-methods: Get log-ratios
getNormTwoChannel-methods: Get Normalized channel data for two channel arrays
getPval-methods: Get p-values
getStat-methods: Retrieve ratio statistics
plotResults-methods: Plot profiles of top genes/probes
rnits: rnits.
Rnits-class: rnits class
summarizeProbes-methods: Summarize probe level data to gene level data
summary-methods: Summary of fit
timeAlign-methods: Curve registration of time series curves
topData-methods: Data of top genes/probes
yeastchemostat: Yeast chemostat data from Ronen and Botstein (Proc Natl Acad...

Functions

$ Man page
$<-,Rnits-method Man page
Rnits-class Man page
Rnits.getLR Man page
build.Rnits Man page Source code
calcYhat Source code
calculateGCV Man page
calculateGCV,Rnits-method Man page
calculateGCV,character,ANY-method Man page
finds0 Source code
fit Man page
fit,Rnits-method Man page
fit,character,ANY-method Man page
getCID Man page
getCID,Rnits-method Man page
getCID,character,ANY-method Man page
getFitModel Man page
getFitModel,Rnits-method Man page
getFitModel,character,ANY-method Man page
getLR Man page
getLR,Rnits-method Man page
getLR,character,ANY-method Man page
getNormTwoChannel Man page
getNormTwoChannel,Rnits-method Man page
getNormTwoChannel,character,ANY-method Man page
getPval Man page
getPval,Rnits-method Man page
getPval,character,ANY-method Man page
getStat Man page
getStat,Rnits-method Man page
getStat,character,ANY-method Man page
getp Source code
modelfit Source code
placeKnots Source code
plotResults Man page
plotResults,Rnits-method Man page
plotResults,character,ANY-method Man page
ranknormalization Source code
rnits Man page
rnits-package Man page
solvemat Source code
studentize Source code
summarizeProbes Man page
summarizeProbes,Rnits-method Man page
summarizeProbes,character,ANY-method Man page
summary,Rnits-method Man page
timeAlign Man page
timeAlign,Rnits-method Man page
timeAlign,character,ANY-method Man page
topData Man page
topData,Rnits-method Man page
topData,character,ANY-method Man page
tsFit Source code
yeastchemostat Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/build-rnits.r
R/calculate-gcv.r
R/fit.r
R/getFitModel.r
R/getLR.r
R/getcid.r
R/getnormtwochannel.r
R/getpval.r
R/getstat.r
R/misc-functions.r
R/plotresults.r
R/rnits-package.r
R/summarize-probes.r
R/summary.r
R/timealign.r
R/topdata.r
R/yeastchemostat-data.r
README.md
build
build/vignette.rds
data
data/yeastchemostat.rda
inst
inst/NEWS
inst/doc
inst/doc/Rnits-vignette.R
inst/doc/Rnits-vignette.Rnw
inst/doc/Rnits-vignette.pdf
man
man/Rnits-class.Rd
man/build.Rnits.Rd
man/calculateGCV-methods.Rd
man/extract-methods.Rd
man/fit-methods.Rd
man/getCID-methods.Rd
man/getFitModel-methods.Rd
man/getLR-methods.Rd
man/getNormTwoChannel-methods.Rd
man/getPval-methods.Rd
man/getStat-methods.Rd
man/plotResults-methods.Rd
man/rnits.Rd
man/summarizeProbes-methods.Rd
man/summary-methods.Rd
man/timeAlign-methods.Rd
man/topData-methods.Rd
man/yeastchemostat.Rd
vignettes
vignettes/Bibliography.bib
vignettes/Rnits-vignette.Rnw
Rnits documentation built on May 20, 2017, 9:20 p.m.

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