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| $-method | List-like accessor methods for ImpulseDE2Object |
| 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 |
| get_boolCaseCtrl | ImpulseDE2Object "get" accession functions |
| get_dfAnnotationProc | ImpulseDE2Object "get" accession functions |
| get_lsModelFits | ImpulseDE2Object "get" accession functions |
| get_matCountDataProc | ImpulseDE2Object "get" accession functions |
| get_scaNProc | ImpulseDE2Object "get" accession functions |
| get_scaQThres | ImpulseDE2Object "get" accession functions |
| get_strReport | ImpulseDE2Object "get" accession functions |
| get_vecAllIDs | ImpulseDE2Object "get" accession functions |
| get_vecConfounders | ImpulseDE2Object "get" accession functions |
| get_vecDispersions | ImpulseDE2Object "get" accession functions |
| get_vecSizeFactors | ImpulseDE2Object "get" accession functions |
| ImpulseDE2 | ImpulseDE2 wrapper |
| ImpulseDE2Object-class | Container class for ImpulseDE2 output |
| list_accession | List-like accessor methods for ImpulseDE2Object |
| names-method | List-like accessor methods for ImpulseDE2Object |
| names.ImpulseDE2Object | 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 |
| set_boolCaseCtrl | ImpulseDE2Object "set" accession functions |
| set_dfAnnotationProc | ImpulseDE2Object "set" accession functions |
| set_dfImpulseDE2Results | ImpulseDE2Object "set" accession functions |
| set_lsModelFits | ImpulseDE2Object "set" accession functions |
| set_matCountDataProc | ImpulseDE2Object "set" accession functions |
| set_scaNProc | ImpulseDE2Object "set" accession functions |
| set_scaQThres | ImpulseDE2Object "set" accession functions |
| set_strReport | ImpulseDE2Object "set" accession functions |
| set_vecAllIDs | ImpulseDE2Object "set" accession functions |
| set_vecConfounders | ImpulseDE2Object "set" accession functions |
| set_vecDEGenes | ImpulseDE2Object "set" accession functions |
| set_vecDispersions | ImpulseDE2Object "set" accession functions |
| set_vecSizeFactors | ImpulseDE2Object "set" accession functions |
| simulateDataSetImpulseDE2 | Simulate a data set for ImpulseDE2 |
| updateDEAnalysis | Update dfImpulseDE2Results after sigmoids have been fit through external call |
| wrapper | ImpulseDE2 wrapper |
| writeReportToFile | Print ImpulseDE2 report to .txt file |
| [[-method | List-like accessor methods for ImpulseDE2Object |