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...
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...
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...
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
makeRPKMsCalculate RPKM and count values on introns and exons from...
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
mycerIds10An 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
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...
rpkmsintron, exons RPKM values of 500 genes from 4sU-seq and...
sfPlotA nice plot to see scaling factors used for RNA-seq and...
simData1repAn INSPEcT object with 1000 simulated rates and concentration...
simData3repAn INSPEcT object with 1000 simulated rates and concentration...
simRatesAn INSPEcT_model object of 1000 simulated rates
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
UCSC_mm9_genes_exonsA Gtf file containing exons definition of 100 genes
UCSC_mm9_genes_intronsA Gtf file containing introns definition of 100 genes
viewModelRatesRetrieve the modeled rates and concentrations
ste-depo/INSPEcT documentation built on Dec. 5, 2017, 12:34 a.m.