flowWorkspace (version 3.16.0)

GatingSetList-class: Class "GatingSetList"

Description

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

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

Usage

GatingSetList(x, samples = NULL)
"rbind2"(x, y = "missing", ...)

Arguments

x

a list of GatingSet

samples

character vector specifying the sample names. if NULL, the sample names are extracted from GatingSets

y

missing not used.

...

other arguments passed to rbind2 method for ncdfFlowList

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

GatingSet GatingHierarchy

Examples

## Not run: 
#     #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
#     getData(gslist2)
#     #get gated flow data from a particular popoulation
#     getData(gslist2, "3+")
# 
#     #extract the gates associated with one popoulation
#     getGate(gslist2,"3+")
#     getGate(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
#     plotGate(gslist2[1:2],5,smooth=T)
#     plotGate_labkey(gslist2[3:4],4,x="<APC Cy7-A>",y="<PE Tx RD-A>",smooth=T)
# 
#     #remove cerntain gates by loop through GatingSets
#     getNodes(gslist2[[1]])
#     lapply(gslist2,function(gs)Rm("Excl",gs))
# 
#     #extract the stats
#     getPopStats(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 rbind2
#     gs_merged2 <- rbind2(gslist2,ncdfFile=path.expand(tempfile(tmpdir="~/rglab/workspace/flowIncubator/output/",fileext=".nc")))
#     gs_merged2
#   ## End(Not run)