Using components at Anduril

Question

[viniciushs88]

Hello,

I'm trying to use a specific component in Anduril.

I have used just R language, now I am really lost with Anduril. It is of course a very basic question, but how can I run this components??? To me this components look like R packages, but I do know how to load or use it.

The only thing that I want is to run this component with examples files ("IN exprMatrix" and "IN cnaMatrix"). I downloaded this Xubuntu at virtual machine available in the site.

With Linux runing, terminal open... then what I do?

anduril run CN2GECollection(exprMatrix=LogMatrix,
                cnaMatrix=CSV,
                exprAnnotation=AnnotationTable,
                //exprRefMatrix=LogMatrix,
                //cnaRefMatrix=CSV,
                //labels=CSV,
                DRImethod="pearson",
                SGRthold=0.1,
                algorithm=<string>,
                ediraMaxseg=50,
                ediraSegment=false,
                endCol="",
                fdrLimit=0.1,
                iClusterK=3,
                iClusterOpt=false,
                locusCol="",
                perm=1000,
                pintArm="",
                pintMethod="pSimCCA",
                scoreLimit=0.1,
                transformType="raw",
                windowSize=10)

Above is the example with default values (which of course do not work and are in a wrong syntax for sure). Thank you very much.

Answer 1

[marko.k.laakso]

CN2GECollection is an Anduril component, which has been implemented in R but is supposed to be used just like any other components in Anduril workflow engine. In your example, an independent component call is confused with a workflow scipt.

Run command executes a complete AndurilScript workflow, which shoud incorporate all component calls. You may simply put the CN2GECollection call into a text file (do not forget the INPUT components pointing to your data files), say cn2ge.and, and call:

anduril run cn2ge.and

Alternatively, run-component command can be used to launch a single component but now the inputs and parameters are given in slightly different format:

anduril run-component -I exprMatrix=mymatrix.csv -I cnaMatrix=myCNAs.csv -P algorithm=pint

... and so forth. In this former case, no INPUTs or other additional components are needed but all the files are taken as command arguments.