Man pages for ste-depo/INSPEcT
Analysis of 4sU-seq and RNA-seq time-course data

AIC-INSPEcT-methodAkaike information criterion calculated for the models...
allcountsA list containing mature and nascent counts for exons and...
chisqmodelRetrieve results of chi-squared test for the selected models
chisqtestRetrieve all results of chi-squared test
combineCombine different Objects of Class INSPEcT
compareSteadyGenerate an object of class INSPEcT_diffsteady from two...
compareSteadyNoNascentCompare mature RNA steady state data
dim-INSPEcT-methodDimensions of an Object of Class INSPEcT
ExtractExtract Parts of an INSPEcT or an INSPEcT_model Object
featureNames-INSPEcT-methodGene Names Associated with an Object of Class INSPEcT
geneClassRetrieve the regulatory class for each gene
getModelGet or replace INSPEcT_model object within INSPEcT object
inHeatmapHeatmap that represent the fold changes of all the five...
INSPEcTINSPEcT package
INSPEcT-classAn S4 class to contain all rates and models generated by...
INSPEcT_diffsteady-classAn S4 class to represent comparisons between two steady-state...
INSPEcT_model-classAn S4 class to represent models generated by INSPEcT
labeledSFAccessor to the slot labeledSF of an INSPEcT object
logLikRetrieve results of log likelihood test
makeModelRatesCalculate modeled rates and concentrations
makeSimDatasetGenerate synthetic rates and concentrations
makeSimModelBuild the synthetic rates shaped on a dataset
modelingParamsGet and set number parameters for the modeling
modelRatesLaunch the modeling process
nascentInspObjAn INSPEcT object without modeled rates and concentrations
nascentInspObj10An INSPEcT object with evaluated and modeled rates and...
newINSPEcTCreate a new INSPEcT object
nGenesGet the number of genes within the INSPEcT object
nTptsGet the number of time points within the INSPEcT object
plotGenePlot the pre-modeled and modeled profiles for one gene
plotMAMA-plot from base means and log fold changes
quantifyExpressionsFromBAMsEvaluate introns and exons expressions from BAM or SAM files
quantifyExpressionsFromTrAbundanceGiven introns and exons abundances (for example RPKMs) this...
quantifyExpressionsFromTrCountsEvaluates introns and exons RPKMs, per gene, from counts...
ratePvalsRetrieve a single p-value for each rate
ratesFirstGuessRetrieve pre-modeling rates and concentrations
ratesFirstGuessVarRetrieve pre-modeling rates and concentrations variance
removeModelremove modelling information from INSPEcT object
rocCurveDisplay rate classification performance
rocThresholdsDisplay rate classification performance with thresholds...
sfPlotA nice plot to see scaling factors used for RNA-seq and...
splitDivide an INSPEcT Object into groups
testingParamsGet or set parameters for model test and selection
totalSFAccessor to the slot totalSF of an INSPEcT object
tptsAccessor to the slot tpts of an INSPEcT object
viewModelRatesRetrieve the modeled rates and concentrations
ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.