Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for Pk/Pf/Pv Master Function
Source:R/MFItoRAU.R
MFItoRAU_Plasmo.RdThis function leverages `MFItoRAU_Pk()` and `MFItoRAU()` to create a final MFI to RAU output for Pk/Pf/Pv analyses.
Arguments
- sero_data
Output of `readserodata_output()`
- plate_list
Output of `readPlateLayout()`
- panel
Panel of Pk/Pf/Pv antigens. Default = "panel1" or user provided csv of Antigens and Species.
- std_point
Standard Point Curve: 5 = 5-point curve, 10 = 10-point curve, "PvLDH" for LDH specific curve. Default = 10. Value is an integer.
- qc_results
Output from `runQC()`.
Value
A list of three data frames: 1. Data frame with MFI data, converted RAU data, matched SampleID's, all intermediate dilution conversion factors 2. Data frame with only SampleID's, MFI and RAU data 3. Data frame #2 in long-format
Examples
# \donttest{
# Example demonstrating multi-plate 5-standard processing workflow.
# These files are included in the SeroTrackR package under inst/extdata.
your_raw_data_5std <- c(
system.file("extdata", "example_MAGPIX_pk_5std_plate1.csv", package = "SeroTrackR"),
system.file("extdata", "example_MAGPIX_pk_5std_plate2.csv", package = "SeroTrackR")
)
your_plate_layout_5std <- system.file(
"extdata", "example_platelayout_pk_5std.xlsx",
package = "SeroTrackR"
)
# Read in raw MAGPIX data
sero_data <- readSeroData(
raw_data = your_raw_data_5std,
platform = "magpix"
)
#> PASS: File example_magpix_pk_5std_plate1.csv successfully validated.
#> PASS: File example_magpix_pk_5std_plate2.csv successfully validated.
# Read matching plate layout
plate_list <- readPlateLayout(
plate_layout = your_plate_layout_5std,
sero_data = sero_data
)
#> Plate layouts correctly identified!
# Quality control
qc_results <- runQC(sero_data, plate_list)
# Run MFI to RAU conversion
mfi_outputs <- MFItoRAU_Plasmo(
sero_data = sero_data,
plate_list = plate_list,
panel = "panel1",
std_point = 5,
qc_results = qc_results
)
# View All Outputs
mfi_outputs
#> $All_Results
#> # A tibble: 168 × 145
#> SampleID Location Location.2 Sample Plate Pk8_MFI Pk8_log_mfi Pk8_max_s1
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 ABC-0001 13(1,B1) B1 Unknown13 plate1 601 6.40 8.63
#> 2 ABC-0002 14(1,B2) B2 Unknown14 plate1 344 5.84 8.63
#> 3 ABC-0003 15(1,B3) B3 Unknown15 plate1 716 6.57 8.63
#> 4 ABC-0004 16(1,B4) B4 Unknown16 plate1 357 5.88 8.63
#> 5 ABC-0005 17(1,B5) B5 Unknown17 plate1 1320 7.19 8.63
#> 6 ABC-0006 18(1,B6) B6 Unknown18 plate1 899 6.80 8.63
#> 7 ABC-0007 19(1,B7) B7 Unknown19 plate1 975 6.88 8.63
#> 8 ABC-0008 20(1,B8) B8 Unknown20 plate1 637 6.46 8.63
#> 9 ABC-0009 21(1,B9) B9 Unknown21 plate1 1635 7.40 8.63
#> 10 ABC-0010 22(1,B10) B10 Unknown22 plate1 256 5.55 8.63
#> # ℹ 158 more rows
#> # ℹ 137 more variables: Pk8_max_dil <dbl>, Pk8_slope <dbl>, Pk8_low_asym <dbl>,
#> # Pk8_upp_asym <dbl>, Pk8_ed50 <dbl>, Pk8_asym_par <dbl>, Pk8_Dilution <dbl>,
#> # PkMSP10_MFI <dbl>, PkMSP10_log_mfi <dbl>, PkMSP10_max_s1 <dbl>,
#> # PkMSP10_max_dil <dbl>, PkMSP10_slope <dbl>, PkMSP10_low_asym <dbl>,
#> # PkMSP10_upp_asym <dbl>, PkMSP10_ed50 <dbl>, PkMSP10_asym_par <dbl>,
#> # PkMSP10_Dilution <dbl>, PkSERA3Ag2_MFI <dbl>, PkSERA3Ag2_log_mfi <dbl>, …
#>
#> $MFI_RAU
#> # A tibble: 168 × 44
#> SampleID Plate Pk8_MFI PkMSP10_MFI PkSERA3Ag2_MFI PkSSP2_MFI `Pv-fam-a_MFI`
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 ABC-0001 plate1 601 346 858 320 389
#> 2 ABC-0002 plate1 344 228. 384 112. 217
#> 3 ABC-0003 plate1 716 584 4397 271 634
#> 4 ABC-0004 plate1 357 235 438. 144. 238
#> 5 ABC-0005 plate1 1320 746 1620 778 746
#> 6 ABC-0006 plate1 899 733 2702. 1015 678.
#> 7 ABC-0007 plate1 975 652 3860 531 716.
#> 8 ABC-0008 plate1 637 228. 1018 459 226.
#> 9 ABC-0009 plate1 1635 1299 1068 795 951
#> 10 ABC-0010 plate1 256 100 534 38 72
#> # ℹ 158 more rows
#> # ℹ 37 more variables: PvMSP5_MFI <dbl>, `PvMSP1-19_MFI` <dbl>,
#> # PvEBP_MFI <dbl>, PvRBP2b_MFI <dbl>, PvCSS_MFI <dbl>, PvPTEX150_MFI <dbl>,
#> # PvMSP8_MFI <dbl>, `PfMSP1-19_MFI` <dbl>, PfAMA1_MFI <dbl>,
#> # Pfetramp5Ag1_MFI <dbl>, PfHSP40Ag1_MFI <dbl>, PfGexp18_MFI <dbl>,
#> # Pk8_Dilution <dbl>, PkMSP10_Dilution <dbl>, PkSERA3Ag2_Dilution <dbl>,
#> # PkSSP2_Dilution <dbl>, `Pv-fam-a_loglog_Dilution` <dbl>, …
#>
#> $MFI_RAU_long
#> # A tibble: 4,200 × 7
#> SampleID Plate Antigens Species MFI RAU RAU_Method
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr>
#> 1 ABC-0001 plate1 Pk8 Pk 601 0.00171 loglog
#> 2 ABC-0001 plate1 PkMSP10 Pk 346 0.0000195 loglog
#> 3 ABC-0001 plate1 PkSERA3Ag2 Pk 858 0.000513 loglog
#> 4 ABC-0001 plate1 PkSSP2 Pk 320 0.00196 loglog
#> 5 ABC-0001 plate1 Pv-fam-a Pv 389 0.0000834 loglog
#> 6 ABC-0001 plate1 Pv-fam-a Pv 389 0.0000923 Adj_loglog
#> 7 ABC-0001 plate1 PvMSP5 Pv 392 0.0000856 loglog
#> 8 ABC-0001 plate1 PvMSP5 Pv 392 0.0000800 Adj_loglog
#> 9 ABC-0001 plate1 PvMSP1-19 Pv 502 0.0000195 loglog
#> 10 ABC-0001 plate1 PvMSP1-19 Pv 502 0.0000762 Adj_loglog
#> # ℹ 4,190 more rows
#>
# }