# Analysis and Visualization of Droplet Digital PCR in R and on the Web

## Documentation for package ‘ddpcr’ version 1.15

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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 | Analysis and visualization of Droplet Digital PCR data.
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)