openCyto working Example: expects {flowWorkspace} but example
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Entering edit mode
Rivka • 0
@rivka-11959
Last seen 4.3 years ago
Munich

Hello,

I've been working with http://isac-net.org/PDFS/c2/c281b4c1-b834-4347-abe5-faa807dd5647.pdf in order to use it for my own data later on.

I have trouble with this part:

#Annotation

keyword_vars<-c("\$FIL","Stim","Sample Order","EXPERIMENT NAME") #relevant keywords
pd<-data.table(getKeywords(gating_set,keyword_vars)) #extract relevant keywords to a data table



earlier in the tutorial gating_set is created, but it is a GatingSet-object.

getKeywords expects it to be a flowWorkspace object.

How is the example working  by calling a GatingSet instead of a flowWorkspace-object? It is not for me.

What am I missing?

Thanks. Rivka

opencyto bioconductor opencyto gating • 552 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 12 days ago

You are right, 'getKeywords' method for 'GatingSet' object is deprecated. You will have to use 'keyword' method on the 'flow data' associated with the 'GatingSet', e.g.

keyword(getData(gating_set),keyword_vars)

Alternatively, you can let 'parseWorkspace' to extract the keyword automatically for you by passing 'keywords' parameter. e.g.

gating_set<-parseWorkspace(ws,name="0882 Samples",path="data/FCS/",keywords = keyword_vars)

See https://github.com/RGLab/flowWorkspace/issues/180 for more details