FCS_clean: FCS_clean function for FCM data

In rprops/Phenoflow_package: Advanced analysis of microbial flow cytometry data

Description

This function denoises a flowSet object using the flowAI package. Observations that #' do not need meet the criteria will be removed. Only works for samples with more than 1000 observations.

Usage

FCS_clean(
  x,
  param = c("FL1-H", "FL3-H", "FSC-H", "SSC-H"),
  timesplit = 0.1,
  TimeChannel = "Time"
)

Arguments

x	flowSet containing the samples to analyse. Cannot have been subsetted to a lower number of parameters.
param	Parameters to base removing of errant observartions on.
timesplit	Fraction of timestep used in flowAI for denoising. Please consult the 'flowAI::flow_auto_qc' function for more information.
TimeChannel	Name of time channel in the FCS files. This can differ between flow cytometers. Defaults to "Time". You can check this by: colnames(flowSet).

Examples

## Full data processing example
data(flowData)
flowData_cleaned <- FCS_clean(flowData[1:3])

rprops/Phenoflow_package documentation built on Sept. 22, 2020, 5:43 p.m.