Package index • PvSTATEM

Core functions

Reading, processing and summarising the data. These functions allow for end-to-end analysis without going into more complex details.

read_luminex_data(): Read Luminex Data

process_plate(): Process a plate and save output values to a CSV

generate_plate_report(): Generate a report for a plate.

Plate and Model classes

Instances of the Plate and Model classes and additional functions for predictions and normalisation. These methods are used to store the data and the model and faciliate the analysis.

Model: Logistic regression model for the standard curve

Plate: Plate object

PlateBuilder: PlateBuilder

create_standard_curve_model_analyte(): Create a standard curve model for a certain analyte

predict(<Model>): Predict the RAU values from the MFI values

get_nmfi(): Calculate normalised MFI values for a plate

Plots

Functions for plotting the data, quality control and the results of the analysis.

plot_counts(): Plot counts in a 96-well plate

plot_layout(): Plot layout of a 96-well plate

plot_mfi_for_analyte(): Plot MFI value distribution for a given analyte

plot_standard_curve_analyte(): Standard curves

plot_standard_curve_analyte_with_model(): Plot standard curve of a certain analyte with fitted model

Helper functions

Additional, lower level functions that are used in the analysis

read_xponent_format(): Read the xPONENT format data

read_intelliflex_format(): Read the Intelliflex format data

read_layout_data(): Read layout data from a file

is_valid_data_type(): Check validity of given data type

is_valid_sample_type(): Check validity of given sample type

translate_sample_names_to_sample_types(): Translate sample names to sample types

handle_high_dose_hook(): Detect and handle the high dose hook effect