2  Pk/Pv/Pf Serology Tutorial

For all of these analyses you can run as many plates as you wish.

2.0.1 Visualisation of the Pk/Pv/Pf Pipeline

library(SeroTrackR)
library(tidyverse)

2.0.2 5-Point Standard Curve

2.0.2.1 Step 1: Load your data!

Firstly, we will be using our example data that’s in-built in the package. Here replace the system.file() argument with the file path for your package.

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")

2.0.2.2 Step 2: Read your data and process MFI to RAU

This function to (a) process raw Serological data and (b) convert MFI to RAU. The runPlasmoPipeline() function will output three data frames:

1. All_Results: All columns of every MFI to RAU conversion
2. MFI_RAU: Just the SampleID, Plate, MFI and RAU values per antigen
3. MFI_RAU_long: SampleID, Plate, MFI, RAU, Antigen, Species (long-format df)

results_5stdcurve <- runPlasmoPipeline(
  raw_data = your_raw_data_5std,
  platform = "magpix",
  plate_layout = your_plate_layout_5std,
  panel = "panel1",
  std_point = 5, 
  experiment_name = "5-point standard curve"
)

2.0.2.2.1 Standard Curve Plot

results_5stdcurve$std_curve

2.0.2.2.2 Bead Counts QC Plot

results_5stdcurve$bead_counts

2.0.2.2.3 Blanks QC Ploat

results_5stdcurve$blanks

2.0.2.2.4 MFI to RAU Tables

All results:

results_5stdcurve$mfi_outputs$All_Results %>%
  head() %>% 
  kable()

MFI and RAU only:

results_5stdcurve$mfi_outputs$MFI_RAU %>%
  head() %>% 
  kable()

MFI and RAU long table:

results_5stdcurve$mfi_outputs$MFI_RAU_long %>%
  head() %>% 
  kable()

2.0.3 10-Point Standard Curve

These steps are very similar to the 5-point standard curve, except where indicated.

2.0.3.1 Step 1: Load your data!

your_raw_data_10std <- c(
  system.file("extdata", "example_MAGPIX_pk_10std_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_pk_10std_plate2.csv", package = "SeroTrackR")
)
your_plate_layout_10std <- system.file("extdata", "example_platelayout_pk_10std.xlsx", package = "SeroTrackR")

2.0.3.2 Step 2: Read your data and process MFI to RAU

results_10stdcurve <- runPlasmoPipeline(
  raw_data = your_raw_data_10std,
  platform = "magpix",
  plate_layout = your_plate_layout_10std,
  panel = "panel1",
  std_point = 10, # here make sure you write 10! 
  experiment_name = "10-point standard curve"
)

2.0.3.2.1 Standard Curve Plot

results_10stdcurve$std_curve

2.0.3.2.2 Bead Counts QC Plot

results_10stdcurve$bead_counts

2.0.3.2.3 Blanks QC Ploat

results_10stdcurve$blanks

2.0.3.2.4 MFI to RAU Tables

All results:

results_10stdcurve$mfi_outputs$All_Results %>%
  head() %>% 
  kable()

MFI and RAU only:

results_10stdcurve$mfi_outputs$MFI_RAU %>%
  head() %>% 
  kable()

MFI and RAU long table:

results_10stdcurve$mfi_outputs$MFI_RAU_long %>%
  head() %>% 
  kable()