Overview of the DRomics package
Introduction | Main workflow | Step 1: importation, check and normalization / transformation of data if needed | General format of imported data | Importation of data from a unique text file | Importation of data as an R object | What types of data can be analyzed using DRomics ? | Description of the classical types of data handled by DRomics | An example with RNAseq data | An example with microarray data | An example with metabolomic data | An example with continuous anchoring apical data | Handling of data collected through specific designs | An example with in situ (observational) RNAseq data | An example with RNAseq data from an experiment with a batch effect | Step 2: selection of significantly responding items | Step 3: fit of dose-response models, choice of the best fit for each curve | Fit of the best model | Plot of fitted curves | Plot of residuals | Description of the family of dose-response models fitted in DRomics | Reminder on least squares regression | Step 4: calculation of benchmark doses (BMD) | Calculation of BMD | Plots of the BMD distribution | Calculation of confidence intervals on the BMDs by bootstrap | Filtering BMDs according to estimation quality | Plot of fitted curves with BMD values and confidence intervals | Plot of all the fitted curves in one figure with points at BMD-BMR values | Description of the outputs of the complete DRomics workflow | Help for biological interpretation of DRomics outputs | Interpretation of DRomics results in a simple case with only one data set obtained in one experimental condition | Augmentation of the data frame of DRomics results with biological annotation | Various plots of results by biological group | BMD ECDF plots split by group defined from biological annotation | Sensitivity plot of biological groups | Trend plot per biological group | Plot of dose-response curves per biological group | Comparison of DRomics results obtained at different experimental levels, for example in a multi-omics approach | Augmentation of the data frames of DRomics results with biological annotation | Binding of the data frames corresponding the results at each experimental level | Comparison of results obtained at the different experimental levels using basic R functions | Comparison of results obtained at the different experimental levels using DRomics functions | ECDF plot of BMD values per group and experimental level using DRomics functions | Plot of the trend repartition per group and experimental level | Sensitivity plot per group and experimental level | Selection of groups on which to focus using the selectgroups() function | BMD ECDF plot with color gradient split by group and experimental level | Plot of the dose-response curves for a selection of groups | References
Rendered fromDRomics_vignette.Rmdusingknitr::rmarkdown