Using components at Anduril
1
0
Entering edit mode
10.5 years ago
viniciushs88 ▴ 50

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.

R Anduril CN2GECollection • 1.8k views
ADD COMMENT
1
Entering edit mode
10.5 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2311 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6