Compute Statistics - flowSet Method

Source: R/cyto_stats_compute-methods.R

Calculate and export flow cytometry statistics for a flowSet.

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

Arguments

x

object of class flowSet.
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.

See also

cyto_stats_compute,flowFrame-method

cyto_stats_compute,GatingSet-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,
  channels = c("Alexa Fluor 488-A", "PE-A"),
  trans = trans,
  stat = "median"
)
#> [[1]]
#>                 Alexa Fluor 488-A     PE-A
#> Activation1.fcs          284.4327 314.0881
#> Activation2.fcs          284.7291 327.8888
#> Activation3.fcs          298.0716 332.8367
#> Activation4.fcs          299.8310 330.3305
#> 
cyto_stats_compute(fs,
  trans = trans,
  stat = "geo mean"
)
#> [[1]]
#>                    FSC-A    FSC-H    FSC-W    SSC-A    SSC-H    SSC-W
#> Activation1.fcs 40932.46 35831.14 74866.43 23625.73 21173.17 73127.03
#> Activation2.fcs 42142.24 36807.03 75035.33 23553.21 21067.52 73268.37
#> Activation3.fcs 41301.94 36032.20 75120.54 23031.80 20548.64 73455.55
#> Activation4.fcs 41823.06 36219.29 75675.59 23470.95 20743.85 74151.72
#>                 Alexa Fluor 488-A     PE-A PE-Texas Red-A  7-AAD-A PE-Cy7-A
#> Activation1.fcs          394.5147 652.2790       131.1220 297.1671 38.70415
#> Activation2.fcs          394.9469 672.1038       113.9421 324.6894 36.76597
#> Activation3.fcs          406.0882 667.9965       106.2362 373.6129 35.16081
#> Activation4.fcs          411.3127 664.3363       105.8318 469.0054 35.45777
#>                 Alexa Fluor 405-A Alexa Fluor 430-A Qdot 605-A
#> Activation1.fcs         1147.5487          756.7397   1375.884
#> Activation2.fcs         1026.3656          670.3747   1271.674
#> Activation3.fcs          987.3453          654.0498   1276.558
#> Activation4.fcs          972.1674          646.6824   1274.180
#>                 Alexa Fluor 647-A Alexa Fluor 700-A APC-Cy7-A     Time
#> Activation1.fcs          1313.115          208.9713  92.58347 2139.517
#> Activation2.fcs          1299.822          216.8302  92.17633 2001.497
#> Activation3.fcs          1479.374          219.8525  95.43460 2021.625
#> Activation4.fcs          1570.542          213.8582  92.73215 2111.609
#> 
cyto_stats_compute(fs,
  stat = "count"
)
#> [[1]]
#>                 count
#> Activation1.fcs 50000
#> Activation2.fcs 50000
#> Activation3.fcs 50000
#> Activation4.fcs 50000
#>