# Serology-Based Data Analysis and Visualization

## Documentation for package ‘SeroTrackR’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

.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
classifyResults | Random Forest Classification
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_BioPlex_PvLDH_plate1_xlsx | Example Serological Dataset: Bioplex PvLDH Plate 1
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
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
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_all | Plot Raw Median Fluorescent Intensity of Standard Curve Data
plotStds_PkPfPv | Plot Raw Median Fluorescent Intensity of Pk/Pf/Pv 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