Analysis and Visualization of Droplet Digital PCR in R and on
the Web
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Documentation for package ‘ddpcr’ version 1.15.2
Help Pages
| analysis_complete | Is the analysis complete? |
| analyze | Run analysis on a ddPCR plate |
| clusters | Potential droplet clusters for a plate type |
| custom_thresholds | Plate type: custom thresholds |
| ddpcr_plate | Plate type: ddPCR plate |
| fam_positive_pnpp | Plate type: FAM-positive PNPP |
| hex_positive_pnpp | Plate type: HEX-positive PNPP |
| launch | Run the interactive analysis tool (Shiny app) in a web browser |
| load_plate | Load a previously saved ddPCR plate |
| name | Plate name |
| name<- | Plate name |
| new_plate | Create a new ddPCR plate |
| next_step | Run the next step in an analysis |
| params | Plate parameters |
| params<- | Plate parameters |
| plate_data | Plate data (droplets data) |
| plate_meta | Plate metadata |
| plate_types | Supported plate types |
| plot.custom_thresholds | Plot a ddPCR plate of type custom thresholds |
| plot.ddpcr_plate | Plot a ddPCR plate |
| plot.wildtype_mutant_pnpp | Plot a ddPCR plate of type wildtype/mutant PNPP |
| pnpp_experiment | Plate type: PNPP experiment |
| reset | Reset a plate |
| sample_data | Get sample data |
| sample_data_dir | Get sample data |
| sample_data_file | Get sample data |
| sample_plate | Get sample data |
| sample_results_file | Get sample data |
| save_plate | Save a ddPCR plate |
| set_default_params | Reset plate parameters to their defaults |
| set_thresholds | Get/set the thresholds |
| steps | Analysis steps of a ddPCR plate |
| subset.ddpcr_plate | Subsetting a ddPCR plate |
| thresholds | Get/set the thresholds |
| thresholds<- | Get/set the thresholds |
| type | Plate type |
| wells_failed | Get successful/failed wells |
| wells_mutant | Get mutant wells |
| wells_negative | Get negative wells |
| wells_positive | Get positive wells |
| wells_success | Get successful/failed wells |
| wells_used | Get wells used in a ddPCR plate |
| wells_wildtype | Get wildtype wells |
| well_info | Get metadata info of a well |
| wildtype_mutant_pnpp | Plate type: wildtype/mutant PNPP |
| x_threshold | Get/set the X threshold |
| x_threshold<- | Get/set the X threshold |
| x_var | Get/set the X/Y variable (dye name) |
| x_var<- | Get/set the X/Y variable (dye name) |
| y_threshold | Get/set the Y threshold |
| y_threshold<- | Get/set the Y threshold |
| y_var | Get/set the X/Y variable (dye name) |
| y_var<- | Get/set the X/Y variable (dye name) |