cyto_stats_compute-flowFrame-method: Compute Statistics - flowFrame Method

In DillonHammill/cytoSuite: Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data

Description

Calculate and export flow cytometry statistics for a flowFrame.

Usage

## S4 method for signature 'flowFrame'
cyto_stats_compute(x, channels = NULL,
  trans = NULL, stat = "median", density_smooth = 1.5)

Arguments

x	object of class flowFrame.
channels	names of of channels for which statistic should be calculated, set to all channels by default.
trans	object of class transformList or transformerList generated by estimateLogicle used to transform the fluorescent channels of x. The transformation list is required to apply the inverse transformation such that the required statistics are returned on the original linear scale.
stat	name of the statistic to calculate, options include "count", "freq", "median", "mode", "mean", "geo mean" or "CV".
density_smooth	smoothing parameter passed to density when calculating mode, set to 1.5 by default.

Author(s)

Dillon Hammill, [e-mail]

See Also

cyto_stats_compute,flowSet-method

Examples

library(CytoRSuiteData)

# Load in samples
fs <- Activation

# Apply compensation
fs <- compensate(fs, fs[[1]]@description$SPILL)

# Transform fluorescent channels
trans <- estimateLogicle(fs[[4]], cyto_fluor_channels(fs))
fs <- transform(fs, trans)

# Compute statistics
cyto_stats_compute(fs[[4]],
  channels = c("Alexa Fluor 647-A", "7-AAD-A"),
  trans = trans,
  stat = "median"
)
cyto_stats_compute(fs[[1]], stat = "count")

DillonHammill/cytoSuite documentation built on March 7, 2019, 10:09 a.m.