Serology-Based Data Analysis and Visualization

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Documentation for package ‘SeroTrackR’ version 1.0.0

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.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