traits_flowcytometer_archive: Gate and extract densities from flowcytometer data by using...

In LEEF-UZH/LEEF.analysis: Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

Gate and extract densities from flowcytometer data by using the archived data

Description

Gate and extract densities from flowcytometer data by using the archived data

Usage

traits_flowcytometer_archive(
  extracted_dir =
    "/Volumes/LEEF-1_archive/LEEF.archived.data/LEEF/3.archived.data/extracted/",
  gates_coordinates,
  timestamps,
  output,
  use_H,
  min_FSC.A,
  log10_all = FALSE,
  particles = c("bacteria", "algae"),
  mc.cores = 1
)

Arguments

extracted_dir	srchive directory of the extracted data
gates_coordinates	the gates_coordinates
timestamps	character vector containing the timestamps to be classified
output	path to which the classified data will be saved as rds
use_H	if TRUE, gating will be done using height, otherwie area
min_FSC.A	numeric. If !NULL, FSA.A <= min_FSC.A will be fitered out by using a rectangular filter flowCore::rectangleGate(filterId="filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))
log10_all	if TRUE, all data not yet log10 transformed will be log10 transformed ("FL2-A", "FL1-H", "FL2-H", "FL3-H", "FL4-H", "FSC-H", "SSC-H") in the same way as in the pipeline.
particles	the particles, as defined in the gates file, to be extracted. Allowed are one or multiple of bacteria, LNA, MNA, HNA, algae
mc.cores	number of cores to be used. Defaults to 1

Value

invisible NULL

LEEF-UZH/LEEF.analysis documentation built on Feb. 8, 2025, 11:18 a.m.