Man pages for INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq data

AIC-INSPEcT-methodAkaike information criterion calculated for the models...
allcountsA list containing mature and nascent counts for exons and...
calculateRatePvalsCalculate a single p-value for each rate
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 an object...
compareSteadyNoNascentIdentify post-transcriptionally regulated genes from an...
computeConfidenceIntervalsCompute confidence intervals
convergenceRetrieve the convergence for the selected models of each gene
correlationPlotDisplay rate classification performance
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
featureWidthsContains two variables: "exWdths" and "intWdths" containing...
geneClassRetrieve the regulatory class for each gene
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...
inspectFromBAMWrapper function from BAM files
inspectFromPCRWrapper function from PCR quantifications
INSPEcT_model-classAn S4 class to represent models generated by INSPEcT
INSPEcT-shinyAppsRun shiny applications contained in the package INSPEcT
INSPEcT_steadyNoNascent-classAn S4 class to represent steady-state analysis without...
labeledSFAccessor to the slot labeledSF of an INSPEcT object
libsizesContains two variables: "nascentLS" and "totalLS" containing...
logLikRetrieve results of log likelihood test
makeModelRatesCalculate modeled rates and concentrations
makeOscillatorySimModelBuild the synthetic rates with oscillatory pattern
makeSimDatasetGenerate synthetic rates and concentrations
makeSimModelBuild the synthetic rates shaped on a dataset
matureGet mature RNA expressions from an object of class...
matureVarGet mature RNA expressions variances from an object of class...
modelingParamsGet and set number parameters for the modeling
modelRatesLaunch the modeling process
modelRatesNFLaunch the modeling process without imposing sigmoid/impulse...
modelSelectionVisualize criteria used for rate variability
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
plotPMgenePlot the premature/mature expression of a gene and the global...
plotPMtrendPlot the premature/mature trend from an object of class...
prematureGet premature RNA expressions from an object of class...
prematureVarGet premature RNA expressions variances from an object of...
processingDelayClassify genes as delayed by the processing using the delta...
PTratioCalculate post-transcriptional ratio from an object of class...
PTregCalculate the post-transcriptional ratio from an object of...
quantifyExpressionsFromBAMsEvaluate introns and exons expressions from BAM or SAM files
quantifyExpressionsFromBWsEvaluate 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...
setConfidenceIntervalsSet confidence intervals
simData3rep_NascentAn INSPEcT object with 1000 simulated rates and concentration...
simData3rep_NoNascentAn INSPEcT object with 1000 simulated rates and concentration...
simData4rep_NascentAn INSPEcT object with 1000 simulated rates and concentration...
simData4rep_NoNascentAn INSPEcT object with 1000 simulated rates and concentration...
splitDivide an INSPEcT Object into groups
tptsAccessor to the slot tpts of an INSPEcT object
viewConfidenceIntervalsRetrieve the modeled Confidence Intervals
viewModelRatesRetrieve the modeled rates and concentrations
INSPEcT documentation built on Nov. 8, 2020, 6:49 p.m.