On boolean combinations (flowWorkspace)
0
0
Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 14 months ago

Three ways of doing this:

1. add a boolean gate to the existing GatingSet

    #say you want a combination of cytokine gates: '4+/IFNg', '4+/TNFa', '4+/IL2'
#simply construct a booleanFilter object
boolgate <- booleanFilter(4+/IFNg & 4+/TNFa & 4+/IL2)
#  or
char2booleanFilter("4+/IFNg & 4+/TNFa & 4+/IL2") # takes a character as input which is more programmatic
#then add to GatingSet, if name is not supplied, then the entire expression string is used to name the new gate

add(gs, boolgate, parent="4+", name = "myBool")
#compute the gate
recompute(gs, "myBool")
#get the count
getTotal(gs, "myBool")
#delete the gate if it is no longer needed
Rm("myBool", gs)

2. or there is one wrapper function does all the above steps in one call

    #calculate boolean indices
ind.list <- getIndices(gs,quote(4+/IFNg & 4+/TNFa & 4+/IL2))
#count the events
count <- lapply(ind.list, function(ind)length(which(ind)))

3. if you don't like the idea of adding new gates, you can grab the event indices from each gate and do the boolean operations on them

    #get indices for each gate
ind1.list <- getIndice((gs, 'cd4/IFNg')
ind2.list <- getIndice((gs, 'cd4/TNFa')
ind3.list <- getIndice((gs, 'cd4/IL2')
#combine these indices
ind.list <- mapply(ind1.list, ind2.list, ind3.list, FUN = function(ind1, ind2,ind3)ind1&ind2&ind3)
#count events
count <- lapply(ind.list, function(ind)length(which(ind)))

On 05/29/2015 02:29 AM, John Aponte wrote:

Dear Mike,

We would need to calculate the number of events for boolean combination of gates. I wonder if you could guide me on how this numbers can be obtained?

Best regards

JJ

--

John J. Aponte

flowworkspace flow cytometry • 1.0k views