Get Count Data from Raw Median Fluorescent Intensity

This function obtains the count data from the raw Median Fluorescent Intensity (MFI). This is an interim function used for the plotCounts function. This function relies on the `readAntigens` and `readSeroData` data processing functions.

Usage

getCounts(processed_counts)

Arguments

processed_counts

Output from `processCounts()`.

Value

(i) Data frame providing bead counts per well per plate. (ii) Designates whether wells should be repeated if there are \(<=\) 15 beads (repeat) or if they are sufficient with > 15 beads (sufficient beads).

Author

Shazia Ruybal-Pesántez, Dionne Argyropoulos

Examples

# \donttest{

# Step 0: Load example raw data
your_raw_data <- c(
  system.file("extdata", "example_MAGPIX_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_plate2.csv", package = "SeroTrackR")
)
your_plate_layout <- system.file(
  "extdata",
  "example_platelayout_1.xlsx",
  package = "SeroTrackR"
)

# Step 1: Read serology data and plate layout
sero_data  <- readSeroData(your_raw_data,"magpix")
#> PASS: File example_magpix_plate1.csv successfully validated.
#> PASS: File example_magpix_plate2.csv successfully validated.
plate_list <- readPlateLayout(your_plate_layout, sero_data)
#> Plate layouts correctly identified!

# Step 2: Process counts and perform quality control
counts      <- processCounts(sero_data)
counts_raw  <- getCounts(counts)
# }