ImpulseDE2Object-class
                        Container class for ImpulseDE2 output
append_strReport        Append string to strReport in ImpulseDE2Object
computeNormConst        Compute a normalisation constant for each
                        sample
computeSizeFactors      Compute a size factor for each sample
estimateImpulseParam    Compute peak and valley impulse model parameter
                        initialisations for data of one gene
estimateSigmoidParam    Compute up and down sigmoid model parameter
                        initialisations for data of one gene
evalImpulse             Compute value of impulse function given
                        parameters.
evalImpulse_comp        Compiled function: evalImpulse
evalLogLikImpulse       Cost function for impulse model
evalLogLikImpulse_comp
                        Compiled function: evalLogLikImpulse
evalLogLikMu            Cost function for constant model
evalLogLikMu_comp       Compiled function: evalLogLikMu
evalLogLikSigmoid       Cost function for sigmoidal model
evalLogLikSigmoid_comp
                        Compiled function: evalLogLikSigmoid
evalSigmoid             Compute value of sigmoidal model given
                        parameters.
evalSigmoid_comp        Compiled function: evalSigmoid
fitConstImpulse         Fits impulse and constant models to all genes
                        on all samples of a condition
fitConstImpulseGene     Fit an impulse and constant model to a single
                        gene
fitConstModel           Fit a constant model to data of a gene
fitImpulseModel         Fit an impulse model to data of a gene
fitModels               Fits impulse and constant models to a
                        timecourse dataset
fitSigmoidGene          Fit a sigmoidal model to a single gene
fitSigmoidModel         Fit a sigmoidal model to data of a gene
fitSigmoidModels        Fits sigmoidal models to all genes on all all
                        samples of a condition
get_accessors           ImpulseDE2Object "get" accession functions
list_accession          List-like accessor methods for ImpulseDE2Object
plotGenes               Plots the impulse fits and data
plotHeatmap             Plot structured z-value heatmaps of
                        differentially expressed genes
processData             Check and process input to runImpulseDE2()
runDEAnalysis           Perform differential expression analysis and
                        identification of transiently activated or
                        deactivated genes.
runDESeq2               Wrapper function for running DESeq2
runImpulseDE2           ImpulseDE2 wrapper
set_accessors           ImpulseDE2Object "set" accession functions
simulateDataSetImpulseDE2
                        Simulate a data set for ImpulseDE2
updateDEAnalysis        Update dfImpulseDE2Results after sigmoids have
                        been fit through external call
writeReportToFile       Print ImpulseDE2 report to .txt file
