R Normalization and Inference of Time Series data

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Documentation for package ‘Rnits’ version 1.40.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

rnits-package	rnits.
$	replace slot of Rnits
$<--method	replace slot of Rnits
build.Rnits	Input the RGlist raw data, build a Rnits object and perform filtering and normalization
calculateGCV	Calculate the optimal B-spline model using generalized cross-validation
calculateGCV-method	Calculate the optimal B-spline model using generalized cross-validation
fit	Fit model on time series data
fit-method	Fit model on time series data
getCID	Cluster IDs of probes/genes from fitted 'Rnits'
getCID-method	Cluster IDs of probes/genes from fitted 'Rnits'
getFitModel	Extract fit data from 'Rnits' object
getFitModel-method	Extract fit data from 'Rnits' object
getLR	Get log-ratios
getLR-method	Get log-ratios
getNormTwoChannel	Get Normalized channel data for two channel arrays
getNormTwoChannel-method	Get Normalized channel data for two channel arrays
getPval	Get p-values
getPval-method	Get p-values
getStat	Retrieve ratio statistics
getStat-method	Retrieve ratio statistics
plotResults	Plot profiles of top genes/probes
plotResults-method	Plot profiles of top genes/probes
rnits	rnits.
Rnits-class	rnits class
Rnits.getLR	Get log-ratios
summarizeProbes	Summarize probe level data to gene level data
summarizeProbes-method	Summarize probe level data to gene level data
summary-method	Summary of fit
timeAlign	Curve registration of time series curves
timeAlign-method	Curve registration of time series curves
topData	Data of top genes/probes
topData-method	Data of top genes/probes
yeastchemostat	Yeast chemostat data from Ronen and Botstein (Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):389-94. Epub 2005 Dec 28.)