Package index • SeroTrackR

Global Functions

Pipelines

Functions that contain entire processing pipelines.

runLDHPipeline(): Run LDH Pipeline from Start to End
runPlasmoPipeline(): Run Pk/Pf/Pv Data Analysis Pipeline from Start to End
runPvSeroPipeline(): Run PvSero Pipeline from Start to End

Data Processing

Plate Handling

Process raw Luminex data and plate layouts.

readSeroData(): Read Raw Serological Data
readPlateLayout(): Read Plate Layout/s
getPlateLayout(): Find and create a master plate layout file

Quality Control

Quality control checking functions.

runQC(): Run Quality Control Pipeline
getRepeats(): Check Beads to Repeat
plotBeadCounts(): Plot Bead Counts per Plate per Antigen
plotBlanks(): Plot Raw Median Fluorescent Intensity Blanks Data
plotBoxPlotClassification(): Plot Classification
plotCounts(): Plot Bead Count Data
plotMFI(): Median Fluorescent Intensity (MFI) Box Plots
plotModel(): Plot the Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) Results Data
plotModel_Adj(): Plot the Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) Results Data based on ETH standard
plotRAU(): Relative Antibody Unit (RAU) Box Plots
plotStds(): Plot Raw Median Fluorescent Intensity of Standard Curve Data
plotStds_PkPfPv(): Plot Raw Median Fluorescent Intensity of Pk/Pf/Pv Standard Curve Data
plotStds_all(): Plot Raw Median Fluorescent Intensity of Standard Curve Data
processPkPfPv(): Processing Serological Data for Pk/Pf/Pv MFI to RAU conversion
renderQCReport(): Generate QC PDF Report

MFI to RAU Conversion

Functions for converting MFI to RAU.

MFItoRAU(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion
MFItoRAU_Adj(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion based on other standard
MFItoRAU_LDH(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for LDH
MFItoRAU_Pk(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for Pk proteins
MFItoRAU_Plasmo(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for Pk/Pf/Pv Master Function

Machine Learning Algorithm

Classification

Classify serological data.

classifyResults(): Random Forest Classification
plotBoxPlotClassification(): Plot Classification
renderClassificationTable(): All Classification Data

Internals

Internal helpers

Internal functions and helpers.

MFItoRAU(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion
MFItoRAU_Adj(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion based on other standard
MFItoRAU_LDH(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for LDH
MFItoRAU_Pk(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for Pk proteins
MFItoRAU_Plasmo(): Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for Pk/Pf/Pv Master Function
classifyResults(): Random Forest Classification
.check_platform(): Check Platform
.clean_bioplex(): Helper function to process bioplex data
.clean_luminex(): Helper function to process luminex (Magpix/Intelliflex) data
.convert_dilution_to_mfi(): Convert known dilution to mfi from fitted standard curve
.convert_mfi_to_dilution(): Convert mfi to dilution using known standard curve fit.
.convert_mfi_to_dilution_no_bounds(): Convert mfi to dilution using known standard curve fit and no bounds
.convert_mfi_to_dilution_no_lower_bound(): Convert mfi to dilution using known standard curve fit and no lower bound
.extract_luminex_sections(): Helper function to process luminex sections
.fit_standard_curve(): Fit a standard curve to known mfi and dilution values.
.magpix_version_config(): Helper function to identify Magpix version
.merge_mfitorau(): Helper function to add Sample IDs to output.
.post_process_bioplex(): Helper function to process bioplex sections
.post_process_luminex(): Helper function to process luminex into master_list
.process_antigen_loglog(): Helper function to fit a 5-parameter logistic standard curve to dilutions
.read_luminex_file(): Helper function to read raw luminex files
.relabel_columns(): Relabel column names to Standardised Naming Convention
.setup_mfitorau_inputs(): Helper function to set up MFI to RAU function
example_BioPlex_PvLDH_plate1_xlsx: Example Serological Dataset: Bioplex PvLDH Plate 1
example_BioPlex_plate1_xlsx: Example Serological Dataset: Bioplex Plate 1
example_BioPlex_plate2_xlsx: Example Serological Dataset: Bioplex Plate 2
example_BioPlex_plate3_xlsx: Example Serological Dataset: Bioplex Plate 3
example_MAGPIX_pk_10std_plate1_csv: Example Serological Dataset: MAGPIX Plate 1 Pk Analysis 10-Point Standard Curve A dataset containing raw MFI values and metadata from a sample plate run (MAGPIX).
example_MAGPIX_pk_10std_plate2_csv: Example Serological Dataset: MAGPIX Plate 2 Pk Analysis 10-Point Standard Curve
example_MAGPIX_pk_5std_plate1_csv: Example Serological Dataset: MAGPIX Plate 1 Pk Analysis 5-Point Standard Curve A dataset containing raw MFI values and metadata from a sample plate run (MAGPIX).
example_MAGPIX_pk_5std_plate2_csv: Example Serological Dataset: MAGPIX Plate 2 Pk Analysis 5-Point Standard Curve
example_MAGPIX_plate1_csv: Example Serological Dataset: MAGPIX Plate 1 A dataset containing raw MFI values and metadata from a sample plate run (MAGPIX).
example_MAGPIX_plate2_csv: Example Serological Dataset: MAGPIX Plate 2
example_MAGPIX_plate3_csv: Example Serological Dataset: MAGPIX Plate 3
example_platelayout_1_xlsx: 96 Well Plate Example Layout
example_platelayout_pk_10std_xlsx: 10-Point Standard Curve Example Plate Layout
example_platelayout_pk_5std_xlsx: 5-Point Standard Curve Example Plate Layout
getAntigenCounts(): Get Count Data for each Antigen from the Raw Median Fluorescent Intensity
getCounts(): Get Count Data from Raw Median Fluorescent Intensity
getCountsQC(): Get All Counts Data
getGithubRelease(): Get GitHub Version
getPlateLayout(): Find and create a master plate layout file
getRepeats(): Check Beads to Repeat
getSampleID(): Get SampleID from Plate Layout
makeCard(): Make Card in Fluent UI
plotBeadCounts(): Plot Bead Counts per Plate per Antigen
plotBlanks(): Plot Raw Median Fluorescent Intensity Blanks Data
plotBoxPlotClassification(): Plot Classification
plotCounts(): Plot Bead Count Data
plotMFI(): Median Fluorescent Intensity (MFI) Box Plots
plotModel(): Plot the Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) Results Data
plotModel_Adj(): Plot the Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) Results Data based on ETH standard
plotRAU(): Relative Antibody Unit (RAU) Box Plots
plotStds(): Plot Raw Median Fluorescent Intensity of Standard Curve Data
plotStds_PkPfPv(): Plot Raw Median Fluorescent Intensity of Pk/Pf/Pv Standard Curve Data
plotStds_all(): Plot Raw Median Fluorescent Intensity of Standard Curve Data
processCounts(): Process Counts from Raw Serological Data file
processPkPfPv(): Processing Serological Data for Pk/Pf/Pv MFI to RAU conversion
readPlateLayout(): Read Plate Layout/s
readSeroData(): Read Raw Serological Data
renderClassificationTable(): All Classification Data
renderDetailsList(): Create a Fluent UI Table
renderQCReport(): Generate QC PDF Report
renderReport(): Render Markdown report
renderTwoCols(): Create two columns in Fluent UI
runLDHPipeline(): Run LDH Pipeline from Start to End
runPlasmoPipeline(): Run Pk/Pf/Pv Data Analysis Pipeline from Start to End
runPvSeroPipeline(): Run PvSero Pipeline from Start to End
runQC(): Run Quality Control Pipeline