Man pages for ddpcr
Analysis and Visualization of Droplet Digital PCR in R and on the Web

analysis_completeIs the analysis complete?
analyzeRun analysis on a ddPCR plate
bind_df_endsHelper function for move_front and move_back
calc_negative_freq_simpleCalculate negative frequency based on number of drops
calculate_concentrationCalculate template concentration
calculate_concentration_singleCalculate concentration in a single well
calculate_negative_freqsCalculate negative frequencies in whole plate
calculate_neg_freq_singleCalculate negative frequency of a single well
capitalizeCapitalize the first letter of a string
cat0Concatenate strings with no space between them
check_stepEnsure the plate's status is at the right step
classify_dropletsAnalysis step: Classify droplets
classify_droplets.pnpp_experimentAnalysis step: Classify droplets
classify_droplets_singleClassify droplets in a well
classify_droplets_single.pnpp_experimentClassify droplets in a well
classify_thresholdsAnalysis step: Classify droplets
clusterGet cluster ID by name
cluster_nameGet cluster name by ID
clustersPotential droplet clusters for a plate type
col_to_numConvert a plate column to a number
custom_thresholdsPlate type: custom thresholds
ddpcrAnalysis and visualization of Droplet Digital PCR data.
ddpcr_platePlate type: ddPCR plate
define_clustersDefine droplet clusters
define_clusters.custom_thresholdsDefine droplet clusters for custom thresholds plates
define_clusters.ddpcr_plateDefine droplet clusters for default plates
define_clusters.pnpp_experimentDefine droplet clusters for PNPP experiments
define_paramsDefine plate type parameters
define_params.custom_thresholdsDefine plate type parameters for custom thresholds plates
define_params.ddpcr_plateDefine plate type parameters for default plates
define_params.fam_positive_pnppDefine plate type parameters for FAM-positive PNPP
define_params.hex_positive_pnppDefine plate type parameters for HEX-positive PNPP
define_params.pnpp_experimentDefine plate type parameters for PNPP experiments
define_params.wildtype_mutant_pnppDefine plate type parameters for wildtype/mutant PNPP
define_stepsDefine analysis steps
define_steps.custom_thresholdsDefine analysis steps for custom thresholds plates
define_steps.ddpcr_plateDefine analysis steps for default plates
define_steps.pnpp_experimentDefine analysis steps for PNPP experiments
diff.point2dEuclidean distance between two points
err_msgShow an error message
fam_positive_pnppPlate type: FAM-positive PNPP
get_colGet column from well ID
get_empty_cutoffGet the cutoff for empty droplets in a well
get_empty_cutoff.ddpcr_plateGet the cutoff for empty droplets in a well
get_empty_cutoff.pnpp_experimentGet the cutoff for empty droplets in a well
get_filled_borderGet border of filled droplets in PNPP experiment
get_filled_dropsGet filled droplets in PNPP experiment
get_outlier_cutoffGet the cutoff for outliers
get_outlier_cutoff.ddpcr_plateGet the cutoff for outliers
get_rowGet row from well ID
get_single_wellGet droplet data from a well
get_wells_btwnGet all wells between two wells (assume a rectangle layout)
grapes-btwn-grapesDetermine if a numeric value is within a range
grapes-greater-than-grapesmagrittr forward-pipe operator
has_signif_negative_clusterDoes a well have a statistically significant number of...
has_stepDoes a ddPCR plate have a step with this name?
hex_positive_pnppPlate type: HEX-positive PNPP
is_dirDetermine if a given path is a valid directory
is_dirtyIs the plate object dirty (ie has changed since the analysis...
is_empty_plateIs a plate empty?
is_fileDetermine if a given path is a valid file
is_rangeIs the given parameter a range?
is_well_successDetermine if a well had a successful ddPCR run
is_well_success.ddpcr_plateDetermine if a well had a successful ddPCR run
is_well_success.pnpp_experimentDetermine if a well had a successful ddPCR run
launchRun the interactive analysis tool (Shiny app) in a web...
load_plateLoad a previously saved ddPCR plate
local_maximaGet the indices of the local maxima in a list of numbers
local_minimaGet the indices of the local minima in a list of numbers
lol_to_dfConvert a list of lists returned from vapply to a dataframe
mark_clustersMark the clusters of droplets only in certain wells to their...
merge_dfs_overwrite_colOverwrite a column in a data.frame based on a matching column...
meta_var_nameName of variable in PNPP experiment metadata
move_backMove columns to the back of a data.frame
move_frontMove columns to the front of a data.frame
msgWrite a message to the user if the 'ddpcr.verbose' option is...
namePlate name
named_vec_to_dfConvert a named vector returned from vapply to a dataframe
new_plateCreate a new ddPCR plate
next_stepRun the next step in an analysis
normalize_to_rdsNormalize a file name to .rds suffix
num_to_colConvert a number to plate column
num_to_rowConvert a number to plate row
other_dimGiven an axis (X or Y), return the other
paramsPlate parameters
parent_plate_typeParent plate type
parent_plate_type.ddpcr_plateParent plate type of default plates
parent_plate_type.defaultParent plate type of any plate
parent_plate_type.fam_positive_pnppParent plate type of FAM-positive PNPP
parent_plate_type.hex_positive_pnppParent plate type of HEX-positive PNPP
parent_plate_type.wildtype_mutant_pnppParent plate type of wildtype/mutant PNPP
plate_dataPlate data (droplets data)
plate_data-setOverwrite the plate data
plate_metaPlate metadata
plate_meta-setOverwrite the plate metadata
plate_typesSupported plate types
plot.custom_thresholdsPlot a ddPCR plate of type custom thresholds
plot.ddpcr_platePlot a ddPCR plate
plot.pnpp_experimentPlot a ddPCR plate of type PNPP experiment
plot.wildtype_mutant_pnppPlot a ddPCR plate of type wildtype/mutant PNPP
pnpp_experimentPlate type: PNPP experiment
point2dRepresentation of a 2D point
positive_dimPositive dimension in a PNPP experiment
positive_dim_varName of dye in positive dimension in PNPP experiment
positive_nameName identifier for positive and negative droplets
print.ddpcr_platePrint info about a ddPCR plate
quietSuppress all output from an expression. Works cross-platform.
range_list_to_vecConvert a list of ranges to a vector of its individual...
range_to_endpointsExtract the two endpoints of a range
range_to_seqConvert a range to a vector of all elements between the...
reclassify_dropletsAnalysis step: Reclassify droplets
reclassify_droplets.pnpp_experimentAnalysis step: Reclassify droplets
reclassify_droplets_singleReclassify droplets in a well
reclassify_droplets_single.pnpp_experimentReclassify droplets in a well
remove_emptyAnalysis step: Remove empty droplets
remove_empty.ddpcr_plateAnalysis step: Remove empty droplets
remove_empty.pnpp_experimentAnalysis step: Remove empty droplets
remove_failuresAnalysis step: Remove failed wells
remove_failures.ddpcr_plateAnalysis step: Remove failed wells
remove_outliersAnalysis Step: Remove outlier droplets
remove_outliers.ddpcr_plateAnalysis Step: Remove outlier droplets
resetReset a plate
row_to_numConvert a plate row to a number
sample_dataGet sample data
save_plateSave a ddPCR plate
set_default_paramsReset plate parameters to their defaults
statusPlate status
stepGet step ID by step name
step_beginInform the user that an analysis step is starting
step_endInform the user that an analysis step finished
step_nameGet step name by ID
stepsAnalysis steps of a ddPCR plate
subset.ddpcr_plateSubsetting a ddPCR plate
thresholdsGet/set the thresholds
typePlate type
unanalyzed_clustersGet unanalyzed cluseter IDs
variable_dimVariable dimension in a PNPP experiment
variable_dim_varName of dye in variable dimension in PNPP experiment
warn_msgShow a warning message
WELL_ID_REGEXregex for a well ID
well_infoGet metadata info of a well
wells_mutantGet mutant wells
wells_negativeGet negative wells
wells_positiveGet positive wells
wells_successGet successful/failed wells
wells_usedGet wells used in a ddPCR plate
wells_wildtypeGet wildtype wells
wildtype_mutant_pnppPlate type: wildtype/mutant PNPP
x_thresholdGet/set the X threshold
x_varGet/set the X/Y variable (dye name)
y_thresholdGet/set the Y threshold
ddpcr documentation built on July 8, 2020, 6:49 p.m.