Question: openCyto working Example: expects {flowWorkspace} but example
0
gravatar for Rivka
2.9 years ago by
Rivka0
Munich
Rivka0 wrote:

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

ADD COMMENTlink modified 2.9 years ago by Jiang, Mike1.2k • written 2.9 years ago by Rivka0
Answer: openCyto working Example: expects {flowWorkspace} but example
2
gravatar for Jiang, Mike
2.9 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

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

ADD COMMENTlink written 2.9 years ago by Jiang, Mike1.2k
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