ce.R

library(CytoML)
acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")
#constrct ce object
ce <- cytobankExperiment(acsfile)
ce

## cytobank Experiment:  tcell 
## gatingML File:  /tmp/RtmpKtttqv/file9586a91de74/experiments/3637/cytobank_gate_ml2_v41.xml 
## compensations:  3 
## fcsFiles:  1 
## panels:  1 
## scales:  12

#ce accessors
getCompensationMatrices(ce)[[1]]

##             B710-A      R660-A      R780-A      V450-A     V545-A
## B710-A 1.00000e+00 3.14389e-02 0.190966000 0.003057570 0.00204723
## R660-A 5.53798e-03 1.00000e+00 0.176812000 0.000000000 0.00000000
## R780-A 9.95863e-05 9.84766e-03 1.000000000 0.000000000 0.00000000
## V450-A 0.00000e+00 8.90985e-05 0.000000000 1.000000000 0.45119500
## V545-A 2.47709e-03 5.23516e-04 0.000000000 0.037961500 1.00000000
## G560-A 1.17224e-01 1.64272e-03 0.000332153 0.000000000 0.00000000
## G780-A 1.42052e-02 4.56896e-04 0.175402000 0.000089025 0.00000000
##             G560-A     G780-A
## B710-A 3.44241e-04 0.07193380
## R660-A 0.00000e+00 0.00661890
## R780-A 0.00000e+00 0.03539970
## V450-A 1.08275e-04 0.00000000
## V545-A 6.36181e-05 0.00000000
## G560-A 1.00000e+00 0.00921936
## G780-A 4.09687e-02 1.00000000

getTransformations(ce)

## $`B710-A`
## Transformer:  asinhtGml2 
## 
## $`R660-A`
## Transformer:  asinhtGml2 
## 
## $`R780-A`
## Transformer:  asinhtGml2 
## 
## $`V450-A`
## Transformer:  asinhtGml2 
## 
## $`V545-A`
## Transformer:  asinhtGml2 
## 
## $`G560-A`
## Transformer:  asinhtGml2 
## 
## $`G780-A`
## Transformer:  asinhtGml2 
## 
## attr(,"class")
## [1] "transformerList" "list"

pData(ce)

##                                            name Conditions Individuals
## CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs condition1       ptid1

colnames(ce)

##  [1] "FSC-A"  "FSC-H"  "FSC-W"  "SSC-A"  "B710-A" "R660-A" "R780-A"
##  [8] "V450-A" "V545-A" "G560-A" "G780-A" "Time"

markernames(ce)

## $CytoTrol_CytoTrol_1.fcs
##  [1] "FSC-A"        "FSC-H"        "FSC-W"        "SSC-A"       
##  [5] "CD4"          "CD38 APC"     "CD8 APCH7"    "CD3"         
##  [9] "HLA-DR V500"  "CCR7 PE"      "CD45RA PECy7" "Time"

#parse ce into gs
gs <- cytobank2GatingSet(ce)

pData(gs)

##                                            name Conditions Individuals
## CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs condition1       ptid1

#check stats against csv from acs
statsfile <- ce$attachments[1]
dt_merged <- compare.counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")


all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)

## [1] TRUE