Man pages for ddpcr
Analysis and Visualization of Droplet Digital PCR in R and on the Web
| analysis_complete | Is the analysis complete? |
| analyze | Run analysis on a ddPCR plate |
| bind_df_ends | Helper function for move_front and move_back |
| calc_negative_freq_simple | Calculate negative frequency based on number of drops |
| calculate_concentration | Calculate template concentration |
| calculate_concentration_single | Calculate concentration in a single well |
| calculate_negative_freqs | Calculate negative frequencies in whole plate |
| calculate_neg_freq_single | Calculate negative frequency of a single well |
| capitalize | Capitalize the first letter of a string |
| cat0 | Concatenate strings with no space between them |
| check_step | Ensure the plate's status is at the right step |
| classify_droplets | Analysis step: Classify droplets |
| classify_droplets.pnpp_experiment | Analysis step: Classify droplets |
| classify_droplets_single | Classify droplets in a well |
| classify_droplets_single.pnpp_experiment | Classify droplets in a well |
| classify_thresholds | Analysis step: Classify droplets |
| cluster | Get cluster ID by name |
| cluster_name | Get cluster name by ID |
| clusters | Potential droplet clusters for a plate type |
| col_to_num | Convert a plate column to a number |
| custom_thresholds | Plate type: custom thresholds |
| ddpcr-package | ddpcr: Analysis and Visualization of Droplet Digital PCR in R... |
| ddpcr_plate | Plate type: ddPCR plate |
| define_clusters | Define droplet clusters |
| define_clusters.custom_thresholds | Define droplet clusters for custom thresholds plates |
| define_clusters.ddpcr_plate | Define droplet clusters for default plates |
| define_clusters.pnpp_experiment | Define droplet clusters for PNPP experiments |
| define_params | Define plate type parameters |
| define_params.custom_thresholds | Define plate type parameters for custom thresholds plates |
| define_params.ddpcr_plate | Define plate type parameters for default plates |
| define_params.fam_positive_pnpp | Define plate type parameters for FAM-positive PNPP |
| define_params.hex_positive_pnpp | Define plate type parameters for HEX-positive PNPP |
| define_params.pnpp_experiment | Define plate type parameters for PNPP experiments |
| define_params.wildtype_mutant_pnpp | Define plate type parameters for wildtype/mutant PNPP |
| define_steps | Define analysis steps |
| define_steps.custom_thresholds | Define analysis steps for custom thresholds plates |
| define_steps.ddpcr_plate | Define analysis steps for default plates |
| define_steps.pnpp_experiment | Define analysis steps for PNPP experiments |
| diff.point2d | Euclidean distance between two points |
| err_msg | Show an error message |
| fam_positive_pnpp | Plate type: FAM-positive PNPP |
| get_col | Get column from well ID |
| get_empty_cutoff | Get the cutoff for empty droplets in a well |
| get_empty_cutoff.ddpcr_plate | Get the cutoff for empty droplets in a well |
| get_empty_cutoff.pnpp_experiment | Get the cutoff for empty droplets in a well |
| get_filled_border | Get border of filled droplets in PNPP experiment |
| get_filled_drops | Get filled droplets in PNPP experiment |
| get_outlier_cutoff | Get the cutoff for outliers |
| get_outlier_cutoff.ddpcr_plate | Get the cutoff for outliers |
| get_row | Get row from well ID |
| get_single_well | Get droplet data from a well |
| get_wells_btwn | Get all wells between two wells (assume a rectangle layout) |
| grapes-btwn-grapes | Determine if a numeric value is within a range |
| grapes-greater-than-grapes | magrittr forward-pipe operator |
| has_signif_negative_cluster | Does a well have a statistically significant number of... |
| has_step | Does a ddPCR plate have a step with this name? |
| hex_positive_pnpp | Plate type: HEX-positive PNPP |
| is_dir | Determine if a given path is a valid directory |
| is_dirty | Is the plate object dirty (ie has changed since the analysis... |
| is_empty_plate | Is a plate empty? |
| is_file | Determine if a given path is a valid file |
| is_range | Is the given parameter a range? |
| is_well_success | Determine if a well had a successful ddPCR run |
| is_well_success.ddpcr_plate | Determine if a well had a successful ddPCR run |
| is_well_success.pnpp_experiment | Determine if a well had a successful ddPCR run |
| launch | Run the interactive analysis tool (Shiny app) in a web... |
| load_plate | Load a previously saved ddPCR plate |
| local_maxima | Get the indices of the local maxima in a list of numbers |
| local_minima | Get the indices of the local minima in a list of numbers |
| lol_to_df | Convert a list of lists returned from vapply to a dataframe |
| mark_clusters | Mark the clusters of droplets only in certain wells to their... |
| merge_dfs_overwrite_col | Overwrite a column in a data.frame based on a matching column... |
| meta_var_name | Name of variable in PNPP experiment metadata |
| move_back | Move columns to the back of a data.frame |
| move_front | Move columns to the front of a data.frame |
| msg | Write a message to the user if the 'ddpcr.verbose' option is... |
| name | Plate name |
| named_vec_to_df | Convert a named vector returned from vapply to a dataframe |
| new_plate | Create a new ddPCR plate |
| next_step | Run the next step in an analysis |
| normalize_to_rds | Normalize a file name to .rds suffix |
| num_to_col | Convert a number to plate column |
| num_to_row | Convert a number to plate row |
| other_dim | Given an axis (X or Y), return the other |
| params | Plate parameters |
| parent_plate_type | Parent plate type |
| parent_plate_type.ddpcr_plate | Parent plate type of default plates |
| parent_plate_type.default | Parent plate type of any plate |
| parent_plate_type.fam_positive_pnpp | Parent plate type of FAM-positive PNPP |
| parent_plate_type.hex_positive_pnpp | Parent plate type of HEX-positive PNPP |
| parent_plate_type.wildtype_mutant_pnpp | Parent plate type of wildtype/mutant PNPP |
| plate_data | Plate data (droplets data) |
| plate_data-set | Overwrite the plate data |
| plate_meta | Plate metadata |
| plate_meta-set | Overwrite the 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.pnpp_experiment | Plot a ddPCR plate of type PNPP experiment |
| plot.wildtype_mutant_pnpp | Plot a ddPCR plate of type wildtype/mutant PNPP |
| pnpp_experiment | Plate type: PNPP experiment |
| point2d | Representation of a 2D point |
| positive_dim | Positive dimension in a PNPP experiment |
| positive_dim_var | Name of dye in positive dimension in PNPP experiment |
| positive_name | Name identifier for positive and negative droplets |
| print.ddpcr_plate | Print info about a ddPCR plate |
| quiet | Suppress all output from an expression. Works cross-platform. |
| range_list_to_vec | Convert a list of ranges to a vector of its individual... |
| range_to_endpoints | Extract the two endpoints of a range |
| range_to_seq | Convert a range to a vector of all elements between the... |
| reclassify_droplets | Analysis step: Reclassify droplets |
| reclassify_droplets.pnpp_experiment | Analysis step: Reclassify droplets |
| reclassify_droplets_single | Reclassify droplets in a well |
| reclassify_droplets_single.pnpp_experiment | Reclassify droplets in a well |
| remove_empty | Analysis step: Remove empty droplets |
| remove_empty.ddpcr_plate | Analysis step: Remove empty droplets |
| remove_empty.pnpp_experiment | Analysis step: Remove empty droplets |
| remove_failures | Analysis step: Remove failed wells |
| remove_failures.ddpcr_plate | Analysis step: Remove failed wells |
| remove_outliers | Analysis Step: Remove outlier droplets |
| remove_outliers.ddpcr_plate | Analysis Step: Remove outlier droplets |
| reset | Reset a plate |
| row_to_num | Convert a plate row to a number |
| sample_data | Get sample data |
| save_plate | Save a ddPCR plate |
| set_default_params | Reset plate parameters to their defaults |
| status | Plate status |
| step | Get step ID by step name |
| step_begin | Inform the user that an analysis step is starting |
| step_end | Inform the user that an analysis step finished |
| step_name | Get step name by ID |
| steps | Analysis steps of a ddPCR plate |
| subset.ddpcr_plate | Subsetting a ddPCR plate |
| thresholds | Get/set the thresholds |
| type | Plate type |
| unanalyzed_clusters | Get unanalyzed cluseter IDs |
| variable_dim | Variable dimension in a PNPP experiment |
| variable_dim_var | Name of dye in variable dimension in PNPP experiment |
| warn_msg | Show a warning message |
| WELL_ID_REGEX | regex for a well ID |
| well_info | Get metadata info of a well |
| 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 |
| wildtype_mutant_pnpp | Plate type: wildtype/mutant PNPP |
| x_threshold | Get/set the X threshold |
| x_var | Get/set the X/Y variable (dye name) |
| y_threshold | Get/set the Y threshold |
