# R Normalization and Inference of Time Series data

## Documentation for package ‘Rnits’ version 1.0.0

- 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.)