extract_traits_flowcytometer_archive: Extract traits from flowcytometer data by using the archived...

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

Extract traits from flowcytometer data by using the archived data

Description

Extract traits from flowcytometer data by using the archived data

Usage

extract_traits_flowcytometer_archive(
  extracted_dir =
    "~/Desktop/flowcytometer.FIXED/LEEF.FIXED.archived.data/LEEF/3.archived.data/extracted/",
  gates_coordinates,
  particles = "bacteria",
  timestamps,
  output,
  length_slope,
  length_intercept,
  use_H,
  min_FSC.A,
  log10_all = FALSE,
  mc.cores = 1,
  wellid_keyword = "$WELLID"
)

Arguments

gates_coordinates	the gates_coordinates
particles	particle class to extract. Mainly bacteria or algae, See LEEF.measurement.flowcytometer::extract_traits() for details.
timestamps	character vector containing the timestamps to be classified
output	path to which the classified data will be saved as rds
length_slope	slope of the linear regression of FSC.A and size ( lm(mean_FSC.A ~ diameter_micrometer )
length_intercept	intercept of the linear regression of FSC.A and size ( lm(mean_FSC.A ~ diameter_micrometer )
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.
mc.cores	number of cores to be used. Defaults to 1
wellid_keyword	the kwyword which is used to identify the well ID. Usually "$WELLID" (default), but for the EAWAG Flowcytometer it is "$SMNO".

Value

invisible NULL

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