alias,pop,parent,dims,gating_method,gating_args,collapseDataForGating,groupBy,preprocessing_method,preprocessing_args
boundary,+,root,"FSC-A,SSC-A",boundary,"max = c(250000, 250000)",,,,
singlet,+,boundary,"FSC-A,FSC-H",singletGate,"prediction_level = 0.999, wider_gate = TRUE, subsample_pct = 0.2",,,,
viable,-,singlet,AViD,mindensity,"gate_range = c(500, 1000)",,,,
nonNeutro,-,viable,SSC-A,mindensity,"gate_range = c(50000, 150000)",,,,
DebrisGate,+,nonNeutro,FSC-A,mindensity,"gate_range = c(0, 100000)",,,,
nonDebris,+,viable,FSC-A,refGate,DebrisGate,,,,
lymph,+,nonDebris,"FSC-A,SSC-A",flowClust,"K = 2, quantile = 0.99",,,prior_flowClust,K = 2
cd3,+,lymph,cd3,mindensity,,,,,
*,+/-,cd3,cd8,mindensity,"gate_range = c(1500, 2800), min = 0",,,,
cd4pos,+,cd8-,cd4,mindensity,"gate_range = c(1000, 1500), min = 0",,,,
cd4neg,-,cd8+,cd4,cytokine,"adjust = 2, tol = 0.1",,,,
cd4,+-,cd3,"cd4,cd8",refGate,cd4pos:cd8-,,,,
cd8,-+,cd3,"cd4,cd8",refGate,cd4neg:cd8+,,,,
TNFa,+,cd4,TNFa,cytokine,"adjust = 2, tol = 0.0001",TRUE,PTID:VISITNO,,
TNFa,+,cd8,TNFa,cytokine,"adjust = 2, tol = 0.0001",TRUE,PTID:VISITNO,,
IFNg,+,cd4,IFNg,cytokine,"adjust = 2, tol = 0.0001",TRUE,PTID:VISITNO,,
IFNg,+,cd8,IFNg,cytokine,"adjust = 2, tol = 0.0001",TRUE,PTID:VISITNO,,
IL2,+,cd4,IL2,cytokine,"adjust = 2, tol = 0.001",TRUE,PTID:VISITNO,,
IL2,+,cd8,IL2,cytokine,"adjust = 2, tol = 0.001",TRUE,PTID:VISITNO,,
*,+/-,cd4,cd57,mindensity,"gate_range = c(1000, 3000), min = 0",TRUE,PTID:VISITNO,,
*,+/-,cd8,cd57,mindensity,"gate_range = c(1000, 3000), min = 0",TRUE,PTID:VISITNO,,
prf_gate,+,cd4/cd57-,Perforin,cytokine,"adjust = 2, tol = 0.01",TRUE,PTID:VISITNO,,
prf_gate,+,cd8/cd57-,Perforin,cytokine,"adjust = 2, tol = 0.01",TRUE,PTID:VISITNO,,
Prf,+,cd4,Perforin,refGate,cd4/cd57-/prf_gate,,,,
Prf,+,cd8,Perforin,refGate,cd8/cd57-/prf_gate,,,,
gzb_gate,+,cd4/cd57-,Granzyme,cytokine,"adjust = 2, tol = 1",TRUE,PTID:VISITNO,,
gzb_gate,+,cd8/cd57-,Granzyme,cytokine,"adjust = 2, tol = 1",TRUE,PTID:VISITNO,,
GzB,+,cd4,Granzyme,refGate,cd4/cd57-/gzb_gate,,,,
GzB,+,cd8,Granzyme,refGate,cd8/cd57-/gzb_gate,,,,
cd4 subsets,+,cd4,,polyFunctions,cd4/TNFa:cd4/IFNg:cd4/IL2,,,,
cd8 subsets,+,cd8,,polyFunctions,cd8/TNFa:cd8/IFNg:cd8/IL2,,,,
