Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data
Check if two paths are equal
Clamp a value to a range
Convert dilutions to numeric values
Create a standard curve model for a certain analyte
Remove holes from a vector
Try to detect the format of a file
Convert dilution to RAU
Extract dilution factor from the sample name
Extract dilutions from the layout representation
Extract sample names from layout
Find a layout file given plate filepath
Format dilutions
Generate a Levey-Jennings Report for Multiple Plates.
Generate a report for a plate.
Determine the Join Value
Generate the matrix of plate locations
Calculate normalised MFI values for a plate
Get output directory for a given input file
Handle differences in datetimes
Detect and handle the high dose hook effect
Identify if a file is a MBA data file
Check if a mba format is supported
Check if a value is an outlier
Check validity of given data type
Check validity of given sample type
Check if the vector is monotically decreasing
Check if a value is a scalar
Check if a string is a number
Merge dataframes
Logistic regression model for the standard curve
Plate object
PlateBuilder
Plot counts in a 96-well plate
Plot layout of a 96-well plate
Plot Levey-Jennings chart
Plot MFI value distribution for a given analyte
Plot a 96-well plate with coloured wells
Plot standard curve of a certain analyte with fitted model
Standard curves
Standard curve stacked plot for levey-jennings report
Standard curve thumbnail for report
Predict the RAU values from the MFI values
Process a dir of files to generate normalised data and reports
Process a file to generate normalised data and reports
Process a plate and save output values to a CSV
Read the Intelliflex format data
Read layout data from a file
Read Luminex Data
Read the xPONENT format data
Remove Empty Lists from a List
Select Columns from a DataFrame
Sort a flat list by value
Translate sample names to sample types
Validate filepath and output_dir
Verbose Cat
Verify Character Join
Verify Numeric Join
Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project of the same name - 'PvSTATEM', which is an international project aiming for malaria elimination.
Useful links