Package 'PvSTATEM' reference manual

Title:	Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data
Description:	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.
Authors:	Tymoteusz Kwiecinski [aut, cre] , Jakub Grzywaczewski [aut], Mateusz Nizwantowski [aut], Przemyslaw Biecek [ths] , Nuno Sepulveda [ths]
Maintainer:	Tymoteusz Kwiecinski <[email protected]>
License:	BSD_3_clause + file LICENSE
Version:	0.1.1
Built:	2024-11-08 12:31:03 UTC
Source:	https://github.com/mini-pw/pvstatem

Create a standard curve model for a certain analyte

Description

Create a standard curve model for a certain analyte

Usage

create_standard_curve_model_analyte(
  plate,
  analyte_name,
  data_type = "Median",
  source_mfi_range_from_all_analytes = FALSE,
  detect_high_dose_hook = TRUE,
  ...
)
create_standard_curve_model_analyte(
  plate,
  analyte_name,
  data_type = "Median",
  source_mfi_range_from_all_analytes = FALSE,
  detect_high_dose_hook = TRUE,
  ...
)

Arguments

`plate`	(`Plate()`) Object of the Plate class
`analyte_name`	(`character(1)`) Name of the analyte for which we want to create the model
`data_type`	(`character(1)`) Data type of the value we want to use to fit the model - the same datatype as in the plate file. By default, it equals to `Median`
`source_mfi_range_from_all_analytes`	(`logical(1)`) If `TRUE`, the MFI range is calculated from all analytes; if `FALSE`, the MFI range is calculated only for the current analyte Defaults to `FALSE`
`detect_high_dose_hook`	(`logical(1)`) If `TRUE`, the high dose hook effect is detected and handled. For more information, please see the handle_high_dose_hook function documentation.
`...`	Additional arguments passed to the model Standard curve samples should not contain `na` values in mfi values nor in dilutions.

Value

(Model()) Standard Curve model

Generate a report for a plate.

Description

This function generates a report for a plate. The report contains all the necessary information about the plate, from the general plate parameters, such as examination date, to the breakdown of the analytes' plots. The report is generated using the plate_report_template.Rmd template.

Usage

generate_plate_report(
  plate,
  use_model = TRUE,
  filename = NULL,
  output_dir = "reports",
  counts_lower_threshold = 50,
  counts_higher_threshold = 70,
  additional_notes = NULL
)
generate_plate_report(
  plate,
  use_model = TRUE,
  filename = NULL,
  output_dir = "reports",
  counts_lower_threshold = 50,
  counts_higher_threshold = 70,
  additional_notes = NULL
)

Arguments

`plate`	A plate object.
`use_model`	(`logical(1)`) A logical value indicating whether the model should be used in the report.
`filename`	(`character(1)`) The name of the output HTML report file. If not provided or equals to `NULL`, the output filename will be based on the plate name, precisely: `⁠{plate_name}_report.html⁠`. By default the `plate_name` is the filename of the input file that contains the plate data. For more details please refer to Plate. If the passed filename does not contain `.html` extension, the default extension `.html` will be added. Filename can also be a path to a file, e.g. `path/to/file.html`. In this case, the `output_dir` and `filename` will be joined together. However, if the passed filepath is an absolute path and the `output_dir` parameter is also provided, the `output_dir` parameter will be ignored. If a file already exists under a specified filepath, the function will overwrite it.
`output_dir`	(`character(1)`) The directory where the output CSV file should be saved. Please note that any directory path provided will create all necessary directories (including parent directories) if they do not exist. If it equals to `NULL` the current working directory will be used. Default is 'reports'.
`counts_lower_threshold`	(`numeric(1)`) The lower threshold for the counts plots (works for each analyte). Default is 50.
`counts_higher_threshold`	(`numeric(1)`) The higher threshold for the counts plots (works for each analyte). Default is 70.
`additional_notes`	(`character(1)`) Additional notes to be included in the report. Contents of this fields are left to the user's discretion. If not provided, the field will not be included in the report.

Value

A report.

Examples


plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "PvSTATEM")
# a plate file with reduced number of analytes to speed up the computation
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
note <- "This is a test report.\n**Author**: Jane Doe \n**Tester**: John Doe"

plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)
example_dir <- tempdir(check = TRUE) # a temporary directory
generate_plate_report(plate,
  output_dir = example_dir,
  counts_lower_threshold = 40,
  counts_higher_threshold = 50,
  additional_notes = note
)
plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "PvSTATEM")
# a plate file with reduced number of analytes to speed up the computation
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
note <- "This is a test report.\n**Author**: Jane Doe \n**Tester**: John Doe"

plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)
example_dir <- tempdir(check = TRUE) # a temporary directory
generate_plate_report(plate,
  output_dir = example_dir,
  counts_lower_threshold = 40,
  counts_higher_threshold = 50,
  additional_notes = note
)

Calculate normalised MFI values for a plate

Description

The function calculates the normalised MFI (nMFI) values for each of the analytes in the plate.

The nMFI values are calculated as the ratio of the test samples' MFI values to the standard curve samples with the target dilution.

When nMFI could be used? In general, it is preferred to use Relative Antibody Unit (RAU) values for any analysis. However, it is sometimes impossible to fit a model to the standard curve samples. This may happen if the MFI values of test samples are much higher than the MFI of standard curve samples. Then, the prediction would require significant data extrapolation, which could lead to unreliable results.

In such cases, the nMFI values could be used as a proxy for RAU values if we want, for instance, to account for plate-to-plate variation.

Usage

get_nmfi(
  plate,
  reference_dilution = 1/400,
  data_type = "Median",
  verbose = TRUE
)
get_nmfi(
  plate,
  reference_dilution = 1/400,
  data_type = "Median",
  verbose = TRUE
)

Arguments

`plate`	(`Plate()`) a plate object for which to calculate the nMFI values
`reference_dilution`	(`⁠numeric(1) or character(1)⁠`) the dilution value of the standard curve sample to use as a reference for normalisation. The default is `1/400`. It should refer to a dilution of a standard curve sample in the given plate object. This parameter could be either a numeric value or a string. In case it is a character string, it should have format `⁠1/d+⁠`, where `⁠d+⁠` is any positive integer.
`data_type`	(`character(1)`) type of data for the computation. Median is the default
`verbose`	(`logical(1)`) print additional information. The default is `TRUE`

Value

nmfi (data.frame) a data frame with normalised MFI values for each analyte in the plate and all test samples.

Examples


# read the plate
plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")

plate <- read_luminex_data(plate_file, layout_file)

# artificially bump up the MFI values of the test samples (the Median data type is default one)
plate$data[["Median"]][plate$sample_types == "TEST", ] <-
  plate$data[["Median"]][plate$sample_types == "TEST", ] * 10

# calculate the nMFI values
nmfi <- get_nmfi(plate, reference_dilution = 1 / 400)

# we don't do any extrapolation and the values should be comparable across plates
head(nmfi)
# different params
nmfi <- get_nmfi(plate, reference_dilution = "1/50")

# read the plate
plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")

plate <- read_luminex_data(plate_file, layout_file)

# artificially bump up the MFI values of the test samples (the Median data type is default one)
plate$data[["Median"]][plate$sample_types == "TEST", ] <-
  plate$data[["Median"]][plate$sample_types == "TEST", ] * 10

# calculate the nMFI values
nmfi <- get_nmfi(plate, reference_dilution = 1 / 400)

# we don't do any extrapolation and the values should be comparable across plates
head(nmfi)
# different params
nmfi <- get_nmfi(plate, reference_dilution = "1/50")

Detect and handle the high dose hook effect

Description

Typically, the MFI values associated with standard curve samples should decrease as we dilute the samples. However, sometimes in high dilutions, the MFI presents a non monotonic behavior. In that case, MFI values associated with dilutions above (or equal to) high_dose_threshold should be removed from the analysis.

For the nplr model the recommended number of standard curve samples is at least 4. If the high dose hook effect is detected but the number of samples below the high_dose_threshold is lower than 4, additional warning is printed and the samples are not removed.

The function returns a logical vector that can be used to subset the MFI values.

Usage

handle_high_dose_hook(mfi, dilutions, high_dose_threshold = 1/200)
handle_high_dose_hook(mfi, dilutions, high_dose_threshold = 1/200)

Arguments

`mfi`	(`numeric()`)
`dilutions`	(`numeric()`)
`high_dose_threshold`	(`numeric(1)`) MFI values associated with dilutions above this threshold should be checked for the high dose hook effect

Value

sample selector (logical())

Check validity of given data type

Description

Check if the data type is valid. The data type is valid if it is one of the elements of the VALID_DATA_TYPES vector. The valid data types are:
c(Median, Net MFI, Count, Avg Net MFI, Mean, Peak).

Usage

is_valid_data_type(data_type)
is_valid_data_type(data_type)

Arguments

data_type

A string representing the data type.

Value

TRUE if the data type is valid, FALSE otherwise.

Check validity of given sample type

Description

Check if the sample type is valid. The sample type is valid if it is one of the elements of the VALID_SAMPLE_TYPES vector. The valid sample types are:

c(ALL, BLANK, TEST, NEGATIVE CONTROL, STANDARD CURVE, POSITIVE CONTROL).

Usage

is_valid_sample_type(sample_type)
is_valid_sample_type(sample_type)

Arguments

sample_type

A string representing the sample type.

Value

TRUE if the sample type is valid, FALSE otherwise.

Logistic regression model for the standard curve

Description

The Model class is a wrapper around the nplr model. It allows to predict the RAU (Relative Antibody Unit) values directly from the MFI values of a given sample.

The nplr model is fitted using the formula:

$y = B + \frac{T - B}{(1 + 10^{b \cdot (x_{mid} - x)})^s},$

where:

$y$ is the predicted value, MFI in our case,
$x$ is the independent variable, dilution in our case,
$B$ is the bottom plateau - the right horizontal asymptote,
$T$ is the top plateau - the left horizontal asymptote,
$b$ is the slope of the curve at the inflection point,
$x_{mid}$ is the x-coordinate at the inflection point,
$s$ is the asymmetric coefficient.

This equation is referred to as the Richards' equation. More information about the model can be found in the nplr package documentation.

After the model is fitted to the data, the RAU values can be predicted using the predict method. The RAU value is simply a predicted dilution value (using the standard curve) for a given MFI multiplied by 1,000 000 to have a more readable value. For more information about the differences between dilution, RAU and MFI values, please see the "Normalisation" section in the "Basic PvSTATEM functionalities" vignette.

Public fields

analyte: (character(1))
Name of the analyte for which the model was fitted
dilutions: (numeric())
Dilutions used to fit the model
mfi: (numeric())
MFI values used to fit the model
mfi_min: (numeric(1))
Minimum MFI used for scaling MFI values to the range [0, 1]
mfi_max: (numeric(1))
Maximum MFI used for scaling MFI values to the range [0, 1]
model: (nplr)
Instance of the nplr model fitted to the data
log_dilution: (logical())
Indicator should the dilutions be transformed using the log10 function
log_mfi: (logical())
Indicator should the MFI values be transformed using the log10 function
scale_mfi: (logical())
Indicator should the MFI values be scaled to the range [0, 1]

Active bindings

top_asymptote: (numeric(1))
The top asymptote of the logistic curve
bottom_asymptote: (numeric(1))
The bottom asymptote of the logistic curve

Methods

Method `new()`

Create a new instance of Model R6 class

Usage

Model$new(
  analyte,
  dilutions,
  mfi,
  npars = 5,
  verbose = TRUE,
  log_dilution = TRUE,
  log_mfi = TRUE,
  scale_mfi = TRUE,
  mfi_min = NULL,
  mfi_max = NULL
)

Arguments

analyte: (character(1))
Name of the analyte for which the model was fitted.
dilutions: (numeric())
Dilutions used to fit the model
mfi: MFI (numeric())
values used to fit the model
npars: (numeric(1))
Number of parameters to use in the model
verbose: (logical())
If TRUE prints messages, TRUE by default
log_dilution: (logical())
If TRUE the dilutions are transformed using the log10 function, TRUE by default
log_mfi: (logical())
If TRUE the MFI values are transformed using the log10 function, TRUE by default
scale_mfi: (logical())
If TRUE the MFI values are scaled to the range [0, 1], TRUE by default
mfi_min: (numeric(1))
Enables to set the minimum MFI value used for scaling MFI values to the range [0, 1]. Use values before any transformations (e.g., before the log10 transformation)
mfi_max: (numeric(1))
Enables to set the maximum MFI value used for scaling MFI values to the range [0, 1]. Use values before any transformations (e.g., before the log10 transformation)

Method `predict()`

Predict RAU values from the MFI values

Usage

Model$predict(mfi, over_max_extrapolation = 0, eps = 1e-06)

Arguments

mfi: (numeric())
MFI values for which we want to predict the RAU values
over_max_extrapolation: (numeric(1))
How much we can extrapolate the values above the maximum RAU value seen in standard curve samples $\text{RAU}_{max}$ . Defaults to 0. If the value of the predicted RAU is above $RAU_{max} + \text{over\_max\_extrapolation}$ , the value is censored to the value of that sum.
eps: (numeric(1))
A small value used to avoid numerical issues close to the asymptotes

Returns

(data.frame())
Dataframe with the predicted RAU values for given MFI values The columns are named as follows:

RAU - the Relative Antibody Units (RAU) value
MFI - the predicted MFI value

Method `get_plot_data()`

Data that can be used to plot the standard curve.

Usage

Model$get_plot_data()

Returns

(data.frame())
Prediction dataframe for scaled MFI (or logMFI) values in the range [0, 1]. Columns are named as in the predict method

Method `print()`

Function prints the basic information about the model such as the number of parameters or samples used

Usage

Model$print()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

Model$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples

plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")
plate <- read_luminex_data(plate_file, layout_filepath = layout_file)
model <- create_standard_curve_model_analyte(plate, "S2", log_mfi = TRUE)
print(model)

plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")
plate <- read_luminex_data(plate_file, layout_filepath = layout_file)
model <- create_standard_curve_model_analyte(plate, "S2", log_mfi = TRUE)
print(model)

Plate object

Description

A class to represent the luminex plate. It contains information about the samples and analytes that were examined on the plate as well as some additional metadata and batch info

Public fields

plate_name

(character(1))
Name of the plate. Set to the name of the file from which the plate was read.

analyte_names

(character())
Names of the analytes that were examined on the plate.

sample_names

(character())
Names of the samples that were examined on the plate.

batch_name

(character(1))
Name of the batch to which the plate belongs.

plate_datetime

(POSIXct())
A date and time when the plate was created by the machine

sample_locations

(character())
Locations of the samples on the plate.

sample_types

(character())
Types of the samples that were examined on the plate. The possible values are
c(ALL, BLANK, TEST, NEGATIVE CONTROL, STANDARD CURVE, POSITIVE CONTROL).

dilutions

(character())
A list containing names of the samples as keys and string representing dilutions as values. The dilutions are represented as strings.

dilution_values

(numeric())
A list containing names of the samples as keys and numeric values representing dilutions as values.

default_data_type

(character(1))
The default data type that will be returned by the get_data method. By default is set to Median.

data

(list())
A list containing dataframes with the data for each sample and analyte. The possible data types - the keys of the list are:
c(Median, Net MFI, Count, Avg Net MFI, Mean, Peak).

In each dataframe, the rows represent samples and the columns represent analytes.

batch_info

(list())
A list containing additional, technical information about the batch.

layout

(character())
A list containing information about the layout of the plate. The layout is read from the separate file and usually provides additional information about the dilutions, sample names, and the sample layout on the actual plate.

blank_adjusted

(logical)
A flag indicating whether the blank values have been adjusted.

Methods

Public methods

Plate$new()
Plate$print()
Plate$summary()
Plate$get_data()
Plate$get_dilution()
Plate$get_dilution_values()
Plate$blank_adjustment()
Plate$clone()

Method `new()`

Method to initialize the Plate object

Usage

Plate$new(
  plate_name,
  sample_names,
  analyte_names,
  batch_name = "",
  plate_datetime = NULL,
  sample_locations = NULL,
  sample_types = NULL,
  dilutions = NULL,
  dilution_values = NULL,
  default_data_type = NULL,
  data = NULL,
  batch_info = NULL,
  layout = NULL
)

Arguments

plate_name: (character(1))
Name of the plate. By default is set to an empty string, during the reading process it is set to the name of the file from which the plate was read.
sample_names: (character())
Names of the samples that were examined on the plate.
analyte_names: (character())
Names of the analytes that were examined on the plate.
batch_name: (character(1))
Name of the batch to which the plate belongs. By default is set to an empty string, during the reading process it is set to the batch field of the plate
plate_datetime: (POSIXct())
Datetime object representing the date and time when the plate was created by the machine.
sample_locations: (character())
Locations of the samples on the plate.
sample_types: (character())
Types of the samples that were examined on the plate. The possible values are
c(ALL, BLANK, TEST, NEGATIVE CONTROL, STANDARD CURVE, POSITIVE CONTROL).
dilutions: (character())
A list containing names of the samples as keys and string representing dilutions as values. The dilutions are represented as strings.
dilution_values: (numeric())
A list containing names of the samples as keys and numeric values representing dilutions as values.
default_data_type: (character(1))
The default data type that will be returned by the get_data method. By default is set to Median.
data: (list())
A list containing dataframes with the data for each sample and analyte. The possible data types - the keys of the list are
c(Median, Net MFI, Count, Avg Net MFI, Mean, Peak). In each dataframe, the rows represent samples and the columns represent analytes.
batch_info: (list())
A list containing additional, technical information about the batch.
layout: (character())
A list containing information about the layout of the plate. The layout is read from the separate file and usually provides additional information about the dilutions, sample names, and the sample layout on the actual plate.

Method `print()`

Function prints the basic information about the plate such as the number of samples and analytes

Usage

Plate$print(...)

Arguments

...: Additional parameters to be passed to the print function Print the summary of the plate

Method `summary()`

Function outputs basic information about the plate, such as examination date, batch name, and sample types.

Usage

Plate$summary(..., include_names = FALSE)

Arguments

...: Additional parameters to be passed to the print function Get data for a specific analyte and sample type
include_names: If include_names parameter is TRUE, a part from count of control samples, provides also their names. By default FALSE

Method `get_data()`

Function returns data for a specific analyte and sample.

Usage

Plate$get_data(
  analyte,
  sample_type = "ALL",
  data_type = self$default_data_type
)

Arguments

analyte: An analyte name or its id of which data we want to extract. If set to 'ALL' returns data for all analytes.
sample_type: is a type of the sample we want to extract data from. The possible values are
c(ALL, BLANK, TEST, NEGATIVE CONTROL, STANDARD CURVE, POSITIVE CONTROL). Default value is ALL.
data_type: The parameter specifying which data type should be returned. This parameter has to take one of values:
c(Median, Net MFI, Count, Avg Net MFI, Mean, Peak). What's more, the data_type has to be present in the plate's data Default value is plate's default_data_type, which is usually Median.

Returns

Dataframe containing information about a given sample type and analyte Get the string representation of dilutions

Method `get_dilution()`

Function returns the dilution represented as strings for a specific sample type.

Usage

Plate$get_dilution(sample_type)

Arguments

sample_type: type of the samples that we want to obtain the dilution for. The possible values are
c(ALL, BLANK, TEST, NEGATIVE CONTROL, STANDARD CURVE, POSITIVE CONTROL) Default value is ALL.

Returns

A list containing names of the samples as keys and string representing dilutions as values. Get the numeric representation of dilutions

Method `get_dilution_values()`

Function returns the dilution values for a specific sample type.

Usage

Plate$get_dilution_values(sample_type)

Arguments

sample_type: type of the samples that we want to obtain the dilution values for. The possible values are
c(ALL, BLANK, TEST, NEGATIVE CONTROL, STANDARD CURVE, POSITIVE CONTROL) Default value is ALL.

Returns

A list containing names of the samples as keys and numeric values representing dilutions as values.

Adjust the MFI values by subtracting the background

Method `blank_adjustment()`

Function adjusts the values of samples (all samples excluding the blanks) by clamping the values to the aggregated value of the BLANK samples for each analyte separately.

The purpose of this operation is to unify the data by clamping values below the background noise. how this method works was inspired by the paper https://doi.org/10.1038/s41598-020-57876-0 which covers the quality control in the MBA.

In short, this operation firstly calculates the aggregate of MFI in the BLANK samples (available methods are: min, max, mean, median) and then replaces all values below this threshold with the threshold value.

Method does not modifies the data of type Count.

This operation is recommended to be performed before any further analysis, but is optional. Skipping it before further analysis is allowed, but will result in a warning.

Usage

Plate$blank_adjustment(threshold = "max", in_place = TRUE)

Arguments

threshold: The method used to calculate the background value for each analyte. Every value below this threshold will be clamped to the threshold value. By default max. Available methods are: min, max, mean, median.
inplace: Whether the method should produce new plate with adjusted values or not, By default TRUE - operates on the current plate.

Method `clone()`

The objects of this class are cloneable with this method.

Usage

Plate$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

PlateBuilder

Description

This class helps creating the Plate object. It is used to store the data and validate the final fields.

Active bindings

layout_as_vector: Print the layout associated with the plate as a flattened vector of values.

Methods

Public methods

PlateBuilder$new()
PlateBuilder$set_sample_locations()
PlateBuilder$set_dilutions()
PlateBuilder$set_sample_types()
PlateBuilder$set_sample_names()
PlateBuilder$set_plate_datetime()
PlateBuilder$set_data()
PlateBuilder$set_default_data_type()
PlateBuilder$set_batch_info()
PlateBuilder$set_plate_name()
PlateBuilder$set_layout()
PlateBuilder$build()
PlateBuilder$clone()

Method `new()`

Initialize the PlateBuilder object

Usage

PlateBuilder$new(sample_names, analyte_names, batch_name = "", verbose = TRUE)

Arguments

sample_names

vector of sample names measured during an examination in the same order as in the data

analyte_names

vector of analytes names measured during an examination in the same order as in the data

batch_name

name of the batch during which the plate was examined obtained from the plate info. An optional parameter, by default set to "" - an empty string.

verbose

logical value indicating whether to print additional information. This parameter is stored as a private attribute of the object and reused in other methods

Method `set_sample_locations()`

Set the sample types used during the examination

Usage

PlateBuilder$set_sample_locations(sample_locations)

Arguments

sample_locations: vector of sample locations pretty name ie. A1, B2

Method `set_dilutions()`

Extract and set the dilutions from layout, sample names or use a provided vector of values. The provided vector should be the same length as the number of samples and should contain dilution factors saved as strings

Usage

PlateBuilder$set_dilutions(use_layout_dilutions = TRUE, values = NULL)

Arguments

use_layout_dilutions

logical value indicating whether to use names extracted from layout files to extract dilutions. If set to FALSE the function uses the sample names as a source for dilution

values

a vector of dilutions to overwrite the extraction process

Set and extract sample types from the sample names. Optionally use the layout file to extract the sample types

Method `set_sample_types()`

Usage

PlateBuilder$set_sample_types(use_layout_types = TRUE, values = NULL)

Arguments

use_layout_types: logical value indicating whether to use names extracted from layout files to extract sample types
values: a vector of sample types to overwrite the extraction process

Method `set_sample_names()`

Set the sample names used during the examination. If the layout is provided, extract the sample names from the layout file. Otherwise, uses the original sample names from the Luminex file

Usage

PlateBuilder$set_sample_names(use_layout_sample_names = TRUE)

Arguments

use_layout_sample_names: logical value indicating whether to use names extracted from layout files. If set to false, this function only checks if the sample names are provided in the plate

Method `set_plate_datetime()`

Set the plate datetime for the plate

Usage

PlateBuilder$set_plate_datetime(plate_datetime)

Arguments

plate_datetime: a POSIXct datetime object representing the date and time of the examination

Method `set_data()`

Set the data used during the examination

Usage

PlateBuilder$set_data(data)

Arguments

data

a named list of data frames containing information about the samples and analytes. The list is named by the type of the data e.g. Median, ⁠Net MFI⁠, etc. The data frames contain information about the samples and analytes The rows are different measures, whereas the columns represent different analytes Example of how data$Median looks like:

Sample	Analyte1	Analyte2	Analyte3
Sample1	1.2	2.3	3.4
Sample2	4.5	5.6	6.7
...	...	...	...
Sample96	7.8	8.9	9.0

Method `set_default_data_type()`

Set the data type used for calculations

Usage

PlateBuilder$set_default_data_type(data_type = "Median")

Arguments

data_type: a character value representing the type of data that is currently used for calculations. By default, it is set to Median

Method `set_batch_info()`

Set the batch info for the plate

Usage

PlateBuilder$set_batch_info(batch_info)

Arguments

batch_info: a raw list containing metadata about the plate read from the Luminex file

Method `set_plate_name()`

Set the plate name for the plate. The plate name is extracted from the filepath

Usage

PlateBuilder$set_plate_name(file_path)

Method `set_layout()`

Set the layout matrix for the plate. This function performs basic validation

verifies if the plate is a matrix of shape 8x12 with 96 wells

Usage

PlateBuilder$set_layout(layout_matrix)

Arguments

layout_matrix: a matrix containing information about the sample names. dilutions, etc.

Method `build()`

Create a Plate object from the PlateBuilder object

Usage

PlateBuilder$build(validate = TRUE)

Method `clone()`

The objects of this class are cloneable with this method.

Usage

PlateBuilder$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Plot counts in a 96-well plate

Description

This function plots counts in a 96-well plate using a colour to represent the count ranges. There is a possibility of plotting exact counts in each well.

If the plot window is resized, it's best to re-run the function to adjust the scaling. Sometimes, when a legend is plotted, the whole layout may be shifted. It's best to stretch the window, and everything will be adjusted automatically.

Usage

plot_counts(
  plate,
  analyte_name,
  plot_counts = TRUE,
  plot_legend = FALSE,
  lower_threshold = 50,
  higher_threshold = 70
)
plot_counts(
  plate,
  analyte_name,
  plot_counts = TRUE,
  plot_legend = FALSE,
  lower_threshold = 50,
  higher_threshold = 70
)

Arguments

`plate`	The plate object with the counts data
`analyte_name`	The name of the analyte
`plot_counts`	Logical indicating if the counts should be plotted
`plot_legend`	Logical indicating if the legend should be plotted
`lower_threshold`	The lower threshold for the counts, it separates green and yellow colours
`higher_threshold`	The higher threshold for the counts, it separates yellow and red colours

Value

A ggplot object

Examples

plate_filepath <- system.file("extdata", "CovidOISExPONTENT_CO.csv",
  package = "PvSTATEM", mustWork = TRUE
)
layout_filepath <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx",
  package = "PvSTATEM", mustWork = TRUE
)
plate <- read_luminex_data(plate_filepath, layout_filepath)
plot_counts(
  plate = plate, analyte_name = "OC43_NP_NA",
  plot_counts = TRUE, plot_legend = FALSE
)

plate_filepath <- system.file("extdata", "CovidOISExPONTENT_CO.csv",
  package = "PvSTATEM", mustWork = TRUE
)
layout_filepath <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx",
  package = "PvSTATEM", mustWork = TRUE
)
plate <- read_luminex_data(plate_filepath, layout_filepath)
plot_counts(
  plate = plate, analyte_name = "OC43_NP_NA",
  plot_counts = TRUE, plot_legend = FALSE
)

Plot layout of a 96-well plate

Description

This function plots the layout of a 96-well plate using a colour to represent the sample types.

If the plot window is resized, it's best to re-run the function to adjust the scaling. Sometimes, the whole layout may be shifted when a legend is plotted. It's best to stretch the window, and everything will be adjusted automatically.

Usage

plot_layout(plate, plot_legend = TRUE)
plot_layout(plate, plot_legend = TRUE)

Arguments

`plate`	The plate object with the layout information
`plot_legend`	Logical indicating if the legend should be plotted

Value

A ggplot object

Examples

plate_filepath <- system.file("extdata", "CovidOISExPONTENT_CO.csv",
  package = "PvSTATEM", mustWork = TRUE
)
layout_filepath <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx",
  package = "PvSTATEM", mustWork = TRUE
)
plate <- read_luminex_data(plate_filepath, layout_filepath)
plot_layout(plate = plate, plot_legend = TRUE)

plate_filepath <- system.file("extdata", "CovidOISExPONTENT_CO.csv",
  package = "PvSTATEM", mustWork = TRUE
)
layout_filepath <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx",
  package = "PvSTATEM", mustWork = TRUE
)
plate <- read_luminex_data(plate_filepath, layout_filepath)
plot_layout(plate = plate, plot_legend = TRUE)

Plot MFI value distribution for a given analyte

Description

Plot MFI value distribution for a given analyte

Usage

plot_mfi_for_analyte(
  plate,
  analyte_name,
  data_type = "Median",
  plot_type = "violin",
  scale_y = "log10",
  plot_outliers = FALSE
)
plot_mfi_for_analyte(
  plate,
  analyte_name,
  data_type = "Median",
  plot_type = "violin",
  scale_y = "log10",
  plot_outliers = FALSE
)

Arguments

`plate`	A plate object
`analyte_name`	The analyte to plot
`data_type`	The type of data to plot. Default is "Median"
`plot_type`	The type of plot to generate. Default is "violin". Available options are "boxplot" and "violin".
`scale_y`	What kind of transformation of the scale to apply. By default MFI is presented in a "log10" scale. Available options are described in the documentation of scale_y_continuous under`transform` parameter.
`plot_outliers`	When using "boxplot" type of a plot one can set this parameter to TRUE and display the names of samples for which MFI falls outside the 1.5 IQR interval

Value

A ggplot object

Standard curves

Description

Plot standard curve samples of a plate of a given analyte.

Usage

plot_standard_curve_analyte(
  plate,
  analyte_name,
  data_type = "Median",
  decreasing_rau_order = TRUE,
  log_scale = c("all"),
  plot_line = TRUE,
  plot_blank_mean = TRUE,
  plot_rau_bounds = TRUE,
  plot_legend = TRUE,
  verbose = TRUE
)
plot_standard_curve_analyte(
  plate,
  analyte_name,
  data_type = "Median",
  decreasing_rau_order = TRUE,
  log_scale = c("all"),
  plot_line = TRUE,
  plot_blank_mean = TRUE,
  plot_rau_bounds = TRUE,
  plot_legend = TRUE,
  verbose = TRUE
)

Arguments

`plate`	A plate object
`analyte_name`	Name of the analyte of which standard curve we want to plot.
`data_type`	Data type of the value we want to plot - the same datatype as in the plate file. By default equals to `⁠Net MFI⁠`
`decreasing_rau_order`	If `TRUE` the RAU values are plotted in decreasing order, `TRUE` by default
`log_scale`	Which elements on the plot should be displayed in log scale. By default `"RAU"`. If `NULL` or `c()` no log scale is used, if `"all"` or `c("RAU", "MFI")` all elements are displayed in log scale.
`plot_line`	If `TRUE` a line is plotted, `TRUE` by default
`plot_blank_mean`	If `TRUE` the mean of the blank samples is plotted, `TRUE` by default
`plot_rau_bounds`	If `TRUE` the RAU values bounds are plotted, `TRUE` by default
`plot_legend`	If `TRUE` the legend is plotted, `TRUE` by default
`verbose`	If `TRUE` prints messages, `TRUE` by default

Value

ggplot object with the plot

Plot standard curve of a certain analyte with fitted model

Description

Function plots the values of standard curve samples and the fitted model.

Usage

plot_standard_curve_analyte_with_model(
  plate,
  model,
  data_type = "Median",
  decreasing_rau_order = TRUE,
  log_scale = c("all"),
  plot_asymptote = TRUE,
  plot_test_predictions = TRUE,
  plot_blank_mean = TRUE,
  plot_rau_bounds = TRUE,
  plot_legend = TRUE,
  verbose = TRUE,
  ...
)
plot_standard_curve_analyte_with_model(
  plate,
  model,
  data_type = "Median",
  decreasing_rau_order = TRUE,
  log_scale = c("all"),
  plot_asymptote = TRUE,
  plot_test_predictions = TRUE,
  plot_blank_mean = TRUE,
  plot_rau_bounds = TRUE,
  plot_legend = TRUE,
  verbose = TRUE,
  ...
)

Arguments

`plate`	Plate object
`model`	fitted `Model` object, which predictions we want to plot
`data_type`	Data type of the value we want to plot - the same datatype as in the plate file. By default equals to `Median`
`decreasing_rau_order`	If `TRUE` the RAU values are plotted in decreasing order, `TRUE` by default.
`log_scale`	Which elements on the plot should be displayed in log scale. By default `"all"`. If `NULL` or `c()` no log scale is used, if `"all"` or `c("RAU", "MFI")` all elements are displayed in log scale.
`plot_asymptote`	If `TRUE` the asymptotes are plotted, `TRUE` by default
`plot_test_predictions`	If `TRUE` the predictions for the test samples are plotted, `TRUE` by default The predictions are obtained through extrapolation of the model
`plot_blank_mean`	If `TRUE` the mean of the blank samples is plotted, `TRUE` by default
`plot_rau_bounds`	If `TRUE` the RAU bounds are plotted, `TRUE` by default
`plot_legend`	If `TRUE` the legend is plotted, `TRUE` by default
`verbose`	If `TRUE` prints messages, `TRUE` by default
`...`	Additional arguments passed to the `predict` function

Value

a ggplot object with the plot

Predict the RAU values from the MFI values

Description

More details can be found here: Model

Usage

## S3 method for class 'Model'
predict(object, mfi, ...)
## S3 method for class 'Model'
predict(object, mfi, ...)

Arguments

`object`	(`Model()`) Object of the Model class
`mfi`	(`numeric()`) MFI values for which we want to predict the RAU values Should be in the same scale as the MFI values used to fit the model
`...`	Additional arguments passed to the method

Value

(data.frame())

Process a plate and save output values to a CSV

Description

Depending on the normalisation_type argument, the function will compute the RAU or nMFI values for each analyte in the plate. RAU is the default normalisation type.

The behaviour of the function, in the case of RAU normalisation type, can be summarised as follows:

Adjust blanks if not already done.
Fit a model to each analyte using standard curve samples.
Compute RAU values for each analyte using the corresponding model.
Aggregate computed RAU values into a single data frame.
Save the computed RAU values to a CSV file.

More info about the RAU normalisation can be found in create_standard_curve_model_analyte function documentation create_standard_curve_model_analyte or in the Model reference Model.

In case the normalisation type is nMFI, the function will:

Adjust blanks if not already done.
Compute nMFI values for each analyte using the target dilution.
Aggregate computed nMFI values into a single data frame.
Save the computed nMFI values to a CSV file.

More info about the nMFI normalisation can be found in get_nmfi function documentation get_nmfi.

Usage

process_plate(
  plate,
  filename = NULL,
  output_dir = "normalised_data",
  normalisation_type = "RAU",
  data_type = "Median",
  include_raw_mfi = TRUE,
  adjust_blanks = FALSE,
  verbose = TRUE,
  reference_dilution = 1/400,
  ...
)
process_plate(
  plate,
  filename = NULL,
  output_dir = "normalised_data",
  normalisation_type = "RAU",
  data_type = "Median",
  include_raw_mfi = TRUE,
  adjust_blanks = FALSE,
  verbose = TRUE,
  reference_dilution = 1/400,
  ...
)

Arguments

`plate`	(`Plate()`) a plate object
`filename`	(`character(1)`) The name of the output CSV file with normalised MFI values. If not provided or equals to `NULL`, the output filename will be based on the normalisation type and the plate name, precisely: `⁠{plate_name}_{normalisation_type}.csv⁠`. By default the `plate_name` is the filename of the input file that contains the plate data. For more details please refer to Plate. If the passed filename does not contain `.csv` extension, the default extension `.csv` will be added. Filename can also be a path to a file, e.g. `path/to/file.csv`. In this case, the `output_dir` and `filename` will be joined together. However, if the passed filepath is an absolute path and the `output_dir` parameter is also provided, the `output_dir` parameter will be ignored. If a file already exists under a specified filepath, the function will overwrite it.
`output_dir`	(`character(1)`) The directory where the output CSV file should be saved. Please note that any directory path provided will create all necessary directories (including parent directories) if they do not exist. If it equals to `NULL` the current working directory will be used. Default is 'normalised_data'.
`normalisation_type`	(`character(1)`) type of normalisation to use. Available options are: `c(RAU, nMFI)`.
`data_type`	(`character(1)`) type of data to use for the computation. Median is the default
`include_raw_mfi`	(`logical(1)`) include raw MFI values in the output. The default is `TRUE`. In case this option is `TRUE`, the output dataframe contains two columns for each analyte: one for the normalised values and one for the raw MFI values. The normalised columns are named as `AnalyteName` and `AnalyteName_raw`, respectively.
`adjust_blanks`	(`logical(1)`) adjust blanks before computing RAU values. The default is `FALSE`
`verbose`	(`logical(1)`) print additional information. The default is `TRUE`
`reference_dilution`	(`numeric(1)`) target dilution to use as reference for the nMFI normalisation. Ignored in case of RAU normalisation. Default is `1/400`. It should refer to a dilution of a standard curve sample in the given plate object. This parameter could be either a numeric value or a string. In case it is a character string, it should have the format `⁠1/d+⁠`, where `⁠d+⁠` is any positive integer.
`...`	Additional arguments to be passed to the fit model function (`create_standard_curve_model_analyte`)

Value

a data frame with normalised values

Examples


plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "PvSTATEM")
# a plate file with reduced number of analytes to speed up the computation
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")

plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)

example_dir <- tempdir(check = TRUE) # a temporary directory
# create and save dataframe with computed dilutions
process_plate(plate, output_dir = example_dir)

# process plate without adjusting blanks and save the output to a file with a custom name
process_plate(plate,
  filename = "plate_without_blanks_adjusted.csv",
  output_dir = example_dir, adjust_blanks = FALSE
)


# nMFI normalisation
process_plate(plate,
  output_dir = example_dir,
  normalisation_type = "nMFI", reference_dilution = 1 / 400
)

plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "PvSTATEM")
# a plate file with reduced number of analytes to speed up the computation
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")

plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)

example_dir <- tempdir(check = TRUE) # a temporary directory
# create and save dataframe with computed dilutions
process_plate(plate, output_dir = example_dir)

# process plate without adjusting blanks and save the output to a file with a custom name
process_plate(plate,
  filename = "plate_without_blanks_adjusted.csv",
  output_dir = example_dir, adjust_blanks = FALSE
)


# nMFI normalisation
process_plate(plate,
  output_dir = example_dir,
  normalisation_type = "nMFI", reference_dilution = 1 / 400
)

Read the Intelliflex format data

Description

Read the Intelliflex format data

Usage

read_intelliflex_format(path, verbose = TRUE)
read_intelliflex_format(path, verbose = TRUE)

Arguments

`path`	Path to the INTELLIFLEX file
`verbose`	Print additional information. Default is `TRUE`

Read layout data from a file

Description

Read layout data from a file

Usage

read_layout_data(layout_file_path, ...)
read_layout_data(layout_file_path, ...)

Arguments

`layout_file_path`	Path to the layout file
`...`	Additional arguments to pass to the underlying read function

Value

A matrix with the layout data. The row names are supposed to be letters A,B,C, etc. The column names are supposed to be numbers 1,2,3, etc.

Read Luminex Data

Description

Reads a file containing Luminex data and returns a Plate object. If provided, can also read a layout file, which usually contains information about the sample names, sample types or its dilutions.

The function is capable of reading data in two different formats:

xPONENT
INTELLIFLEX which are produced by two different Luminex machines.

Usage

read_luminex_data(
  plate_filepath,
  layout_filepath = NULL,
  format = "xPONENT",
  plate_file_separator = ",",
  plate_file_encoding = "UTF-8",
  use_layout_sample_names = TRUE,
  use_layout_types = TRUE,
  use_layout_dilutions = TRUE,
  default_data_type = "Median",
  sample_types = NULL,
  dilutions = NULL,
  verbose = TRUE
)
read_luminex_data(
  plate_filepath,
  layout_filepath = NULL,
  format = "xPONENT",
  plate_file_separator = ",",
  plate_file_encoding = "UTF-8",
  use_layout_sample_names = TRUE,
  use_layout_types = TRUE,
  use_layout_dilutions = TRUE,
  default_data_type = "Median",
  sample_types = NULL,
  dilutions = NULL,
  verbose = TRUE
)

Arguments

`plate_filepath`	Path to the Luminex plate file
`layout_filepath`	Path to the Luminex layout file
`format`	The format of the Luminex data. Select from: xPONENT, INTELLIFLEX
`plate_file_separator`	The separator used in the plate file
`plate_file_encoding`	The encoding used in the plate file
`use_layout_sample_names`	Whether to use names from the layout file in extracting sample names.
`use_layout_types`	Whether to use names from the layout file in extracting sample types. Works only when layout file is provided
`use_layout_dilutions`	Whether to use dilutions from the layout file in extracting dilutions. Works only when layout file is provided
`default_data_type`	The default data type to use if none is specified
`sample_types`	a vector of sample types to use instead of the extracted ones
`dilutions`	a vector of dilutions to use instead of the extracted ones
`verbose`	Whether to print additional information and warnings. `TRUE` by default

Value

Plate file containing the Luminex data

Examples

plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")
plate <- read_luminex_data(plate_file, layout_file)

plate_file <- system.file("extdata", "CovidOISExPONTENT_CO.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
# To suppress warnings and additional information use verbose = FALSE
plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)

plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")
plate <- read_luminex_data(plate_file, layout_file)

plate_file <- system.file("extdata", "CovidOISExPONTENT_CO.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
# To suppress warnings and additional information use verbose = FALSE
plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)

Read the xPONENT format data

Description

Read the xPONENT format data

Usage

read_xponent_format(
  path,
  exact_parse = FALSE,
  encoding = "utf-8",
  separator = ",",
  verbose = TRUE
)
read_xponent_format(
  path,
  exact_parse = FALSE,
  encoding = "utf-8",
  separator = ",",
  verbose = TRUE
)

Arguments

`path`	Path to the xPONENT file
`exact_parse`	Whether to parse the file exactly or not Exact parsing means that the batch, calibration and assay metadata will be parsed as well
`encoding`	Encoding of the file
`separator`	Separator for the CSV values
`verbose`	Whether to print the progress. Default is `TRUE`

Translate sample names to sample types

Description

Function translates sample names to sample types based on the sample name from Luminex file and the sample name from the layout file, which may not be provided. The function uses regular expressions to match the sample names to the sample types.

It parses the names as follows:

If sample_names or sample_names_from_layout equals to BLANK, BACKGROUND or B, then SampleType equals to BLANK

If sample_names or sample_names_from_layout equals to ⁠STANDARD CURVE⁠, SC, S, contains substring ⁠1/\d+⁠ and has prefix ⁠ ⁠, S_, S , S or CP3, then SampleType equals to ⁠STANDARD CURVE⁠

If sample_names or sample_names_from_layout equals to ⁠NEGATIVE CONTROL⁠, N, or contains substring NEG, then SampleType equals to ⁠NEGATIVE CONTROL⁠

If sample_names or sample_names_from_layout starts with P followed by whitespace, POS followed by whitespace, some sample name followed by substring ⁠1/\d+⁠ SampleType equals to ⁠POSITIVE CONTROL⁠

Otherwise, the returned SampleType is TEST

Usage

translate_sample_names_to_sample_types(
  sample_names,
  sample_names_from_layout = NULL
)
translate_sample_names_to_sample_types(
  sample_names,
  sample_names_from_layout = NULL
)

Arguments

`sample_names`	(`character()`) Vector of sample names from Luminex file
`sample_names_from_layout`	(`character()`) Vector of sample names from Layout file values in this vector may be different than `sample_names` and may contain additional information about the sample type like dilution. This vector when set has to have at least the length of `sample_names`.

Value

A vector of valid sample_type strings of length equal to the length of sample_names

Examples

translate_sample_names_to_sample_types(c("B", "BLANK", "NEG", "TEST1"))
translate_sample_names_to_sample_types(c("S", "CP3"))

translate_sample_names_to_sample_types(c("B", "BLANK", "NEG", "TEST1"))
translate_sample_names_to_sample_types(c("S", "CP3"))

Package 'PvSTATEM'

Help Index

Create a standard curve model for a certain analyte

Description

Usage

Arguments

Value

Generate a report for a plate.

Description

Usage

Arguments

Value

Examples

Calculate normalised MFI values for a plate

Description

Usage

Arguments

Value

Examples

Detect and handle the high dose hook effect

Description

Usage

Arguments

Value

Check validity of given data type

Description

Usage

Arguments

Value

Check validity of given sample type

Description

Usage

Arguments

Value

Logistic regression model for the standard curve

Description

Public fields

Active bindings

Methods

Public methods

Method new()

Usage

Arguments

Method predict()

Usage

Arguments

Returns

Method get_plot_data()

Usage

Returns

Method print()

Usage

Method clone()

Usage

Arguments

Examples

Plate object

Description

Public fields

Methods

Public methods

Method new()

Usage

Arguments

Method print()

Usage

Arguments

Method summary()

Usage

Arguments

Method get_data()

Usage

Arguments

Returns

Method get_dilution()

Usage

Arguments

Returns

Method get_dilution_values()

Usage

Method `new()`

Method `predict()`

Method `get_plot_data()`

Method `print()`

Method `clone()`

Method `new()`

Method `print()`

Method `summary()`

Method `get_data()`

Method `get_dilution()`

Method `get_dilution_values()`

Method `blank_adjustment()`

Method `clone()`

Method `new()`

Method `set_sample_locations()`

Method `set_dilutions()`

Method `set_sample_types()`

Method `set_sample_names()`

Method `set_plate_datetime()`

Method `set_data()`

Method `set_default_data_type()`

Method `set_batch_info()`

Method `set_plate_name()`

Method `set_layout()`

Method `build()`

Method `clone()`