Man pages for SerolyzeR
Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data
| check_path_equal | Check if two paths are equal |
| clamp | Clamp a value to a range |
| convert_dilutions_to_numeric | Convert dilutions to numeric values |
| create_standard_curve_model_analyte | Create a standard curve model for a certain analyte |
| create_vector_without_holes | Remove holes from a vector |
| detect_mba_format | Try to detect the format of a file |
| dilution_to_rau | Convert dilution to RAU |
| extract_dilution_from_names | Extract dilution factor from the sample name |
| extract_dilutions_from_layout | Extract dilutions from the layout representation |
| extract_sample_names_from_layout | Extract sample names from layout |
| find_layout_file | Find a layout file given plate filepath |
| format_dilutions | Format dilutions |
| format_xlab | Format X-axis label |
| format_ylab | Format Y-axis label |
| generate_levey_jennings_report | Generate a Levey-Jennings Report for Multiple Plates. |
| generate_plate_report | Generate a report for a plate. |
| get_join_value | Determine the Join Value |
| get_location_matrix | Generate the matrix of plate locations |
| get_nmfi | Calculate normalised MFI values for a plate |
| get_output_dir | Get output directory for a given input file |
| handle_datetime | Handle differences in datetimes |
| handle_high_dose_hook | Detect and handle the high dose hook effect |
| is.decreasing | Check if the vector is monotically decreasing |
| is_mba_data_file | Identify if a file is a MBA data file |
| is_mba_format | Check if a mba format is supported |
| is_outlier | Check if a value is an outlier |
| is.scalar | Check if a value is a scalar |
| is.str.number | Check if a string is a number |
| is_valid_data_type | Check validity of given data type |
| is_valid_sample_type | Check validity of given sample type |
| merge_dataframes | Merge dataframes |
| Model | Logistic regression model for the standard curve |
| Plate | Plate Object |
| PlateBuilder | PlateBuilder |
| plot_counts | Plot counts in a 96-well plate |
| plot_layout | Plot layout of a 96-well plate |
| plot_levey_jennings | Plot Levey-Jennings chart |
| plot_mfi_for_analyte | Plot MFI value distribution for a given analyte |
| plot_plate | Plot a 96-well plate with coloured wells |
| plot_standard_curve_analyte | Standard curves |
| plot_standard_curve_analyte_with_model | Plot standard curve of a certain analyte with fitted model |
| plot_standard_curve_stacked | Standard curve stacked plot for levey-jennings report |
| plot_standard_curve_thumbnail | Standard curve thumbnail for report |
| predict.Model | Predict the RAU values from the MFI values |
| process_dir | Process a Directory of Luminex Data Files |
| process_file | Process a File to Generate Normalised Data and Reports |
| process_plate | Process a Plate and Save Normalised Output to CSV |
| read_intelliflex_format | Read the Intelliflex format data |
| read_layout_data | Read layout data from a file |
| read_luminex_data | Read Luminex Data |
| read_xponent_format | Read the xPONENT format data |
| remove_empty_lists | Remove Empty Lists from a List |
| select_columns | Select Columns from a DataFrame |
| sort_list_by | Sort a flat list by value |
| translate_sample_names_to_sample_types | Translate sample names to sample types |
| validate_filepath_and_output_dir | Validate filepath and output_dir |
| verbose_cat | Verbose Cat |
| verify_character_join | Verify Character Join |
| verify_numeric_join | Verify Numeric Join |
