Hi,
I have issues with the getIndices() function from the flowWorkspace package. It identifies much more cells as "TRUE" for a gate than it should. Here's my code:
wspath<-"~/Desktop/workspc.wsp" ws<-openWorkspace(wspath) G <- parseWorkspace(ws,name=1) nodelist<-getNodes(G[[1]]) num_f5<-grep(pattern = paste("/F5$"),nodelist) f5<-nodelist[num_f5] summary(getIndices(G[[1]],f5))
I have no clue why getIndices() doesn't identify the right cells in the gate I'm interested in, it works perfectly for the gates on top of the gate "F5" in my gating strategy.
Thanks in advance,
Helena
If the gates are not parsed correctly, we then need to fix the parsing first. Can you make sure you have the latest version of flowWorkspace package (i.e. 3.20.4)? If so, Can you share your example workspace and FCS for me to trouble shoot? (You can send them to wjiang2@fhcrc.org)