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rnits

R/Bioconductor package for normalization and differential expression inference in time series gene expression microarray data.

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Version

Version

1.6.2

License

GPL-3

Maintainer

Dipen P Sangurdekar

Last Published

February 15th, 2017

Functions in Rnits (1.6.2)

summarizeProbes

Summarize probe level data to gene level data
timeAlign

Curve registration of time series curves
getCID

Cluster IDs of probes/genes from fitted Rnits
build.Rnits

Input the RGlist raw data, build a Rnits object and perform filtering and normalization
getPval

Get p-values
$

replace slot of Rnits
getStat

Retrieve ratio statistics
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.)
topData

Data of top genes/probes
rnits

rnits.
plotResults

Plot profiles of top genes/probes
fit

Fit model on time series data
summary,Rnits-method

Summary of fit
getLR

Get log-ratios
getNormTwoChannel

Get Normalized channel data for two channel arrays
calculateGCV

Calculate the optimal B-spline model using generalized cross-validation
Rnits-class

rnits class
getFitModel

Extract fit data from Rnits object