A list of of GatingSet objects. This class exists for method dispatching.

use GatingSetList constructor to create a GatingSetList from a list of GatingSet

GatingSetList(x, samples = NULL)

Arguments

x

a list of GatingSet

samples

character vector specifying the order of samples. if not specified, the samples are ordered as the underlying stored order.

Details

Objects store a collection of GatingSets,which usually has the same gating trees and markers. Most GatingSets methods can be applied to GatingSetList.

See also

Examples

if (FALSE) { #load several GatingSets from disk gs_list<-lapply(list.files("../gs_toMerge",full=T) ,function(this_folder){ load_gs(this_folder) }) #gs_list is a list gs_groups <- merge(gs_list) #returns a list of GatingSetList objects gslist2 <- gs_groups[[2]] #gslist2 is a GatingSetList that contains multiple GatingSets and they share the same gating and data structure gslist2 class(gslist2) sampleNames(gslist2) #reference a GatingSet by numeric index gslist2[[1]] #reference a GatingSet by character index gslist2[["30104.fcs"]] #loop through all GatingSets within GatingSetList lapply(gslist2,sampleNames) #subset a GatingSetList by [ sampleNames(gslist2[c(4,1)]) sampleNames(gslist2[c(1,4)]) gslist2[c("30104.fcs")] #get flow data from it gs_pop_get_data(gslist2) #get gated flow data from a particular popoulation gs_pop_get_data(gslist2, "3+") #extract the gates associated with one popoulation gs_pop_get_gate(gslist2,"3+") gs_pop_get_gate(gslist2,5) #extract the pheno data pData(gslist2[3:1]) #modify the pheno data pd <- pData(gslist2) pd$id <- 1:nrow(pd) pData(gslist2) <- pd pData(gslist2[3:2]) #plot the gate autoplot(gslist2[1:2],5) #remove cerntain gates by loop through GatingSets gs_get_pop_paths(gslist2[[1]]) lapply(gslist2,function(gs)gs_pop_remove("Excl",gs = gs)) #extract the stats gs_pop_get_count_fast(gslist2) #extract statistics by using getQAStats defined in QUALIFIER package res<-getQAStats(gslist2[c(4,2)],isMFI=F,isSpike=F,nslaves=1) #archive the GatingSetList save_gslist(gslist2, path ="~/rglab/workspace/flowIncubator/output/gslist",overwrite=T) gslist2 <- load_gslist(path ="~/rglab/workspace/flowIncubator/output/gslist") #convert GatingSetList into one GatingSet by merge_list_to_gs gs_merged2 <- merge_list_to_gs(gslist2) gs_merged2 } if (FALSE) { samleNames(gsA) # return A1, A2 samleNames(gsB) # return B1, B2 gs.list <- list(gsA, gsB) gslist<- GatingSetList(gs.list) sampleNames(gslist) #return A1,A2,B1,B2 #set different order when create the GatingSetList gslist<- GatingSetList(gs.list, samples = c("A1","B1", "A2", "B2")) sampleNames(gslist) #return A1,B1,A2,B2 }