fcs_processing: Extract index sorting from flow cytometry data

In rodrigarc/RepertoiR: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Extract index sorting from flow cytometry data

Description

Extracts the Mean Fluoresnce Intensity (MFI) values from the flow cytometry index files (.fcs) and assign specificity to each single-cell sorted well according to the fluorescence intensity of the probes.

Usage

fcs_processing(
  folder_path = "test/test_dataset/fcs_files/",
  compensation = TRUE,
  plate_wells = 96,
  probe1 = "Pre.F",
  probe2 = "Post.F",
  posvalue_probe1 = 600,
  posvalue_probe2 = 400
)

Arguments

folder_path	Folder containing all the flow data index filex (.fcs). Files should be named with their sample/plate ID. eg. "E11_01.fcs"
compensation	Logical argument, TRUE or FALSE, to indicate if the index files were compensated or not. If TRUE, it will apply its compensation prior assigning specificity
plate_wells	Type of plate used for single-cell sorting. eg. "96" or "384"
probe1	Name of the first channel used for the probe or the custom name assigned to the channel in the index file. eg. "FSC.A", "FSC.H", "SSC.A","DsRed.A", "PE.Cy5_5.A", "PE.Cy7.A","BV650.A", "BV711.A","Alexa.Fluor.700.A" "APC.Cy7.A","PerCP.Cy5.5.A","Time"
probe2	Name of the second channel used for the probe or the custom name assigned to the channel in the index file. eg. "FSC.A", "FSC.H", "SSC.A","DsRed.A", "PE.Cy5_5.A", "PE.Cy7.A","BV650.A", "BV711.A","Alexa.Fluor.700.A" "APC.Cy7.A","PerCP.Cy5.5.A","Time"
posvalue_probe1	Threshold used for fluorescence intensities to be considered as positive for the first probe
posvalue_probe2	Threshold used for fluorescence intensities to be considered as positive for the second probe

Value

If saved as an object, it returns a table containing all the processed flow cytometry index files, with their fluorescence intensities for each channel and well position.

Examples

index_sort_data <- fcs_processing(
    folder_path = system.file("/extdata/fcs_index_sorting",
        package = "scifer"
    ),
    compensation = TRUE, plate_wells = 96,
    probe1 = "Pre.F", probe2 = "Post.F",
    posvalue_probe1 = 600, posvalue_probe2 = 400
)

rodrigarc/RepertoiR documentation built on Aug. 14, 2024, 6:29 a.m.