OpenCGA
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Overview

The OpenCGA R Client has been implemented following the Bioconductor guidelines for package development which promote high-quality, well documented and interoperable software. The client provides a user-friendly interface to work with OpenCGA REST Web Services through R.

Client Library

The R package can be downloaded from XXXX and the source code can be found in YYYYY. The methods and classes implemented have been designed following the S4 interface as recommended by Bioconductor. Class definitions are stored in R/AllClasses.R. Currently, there is only one class defined containing the OpenCGA connection details which is extensively used by all methods in the package. A set of methods have been implemented to deal with the connectivity and login to the REST host. These methods are stored in R/OpencgaR-methods.R.

Initialise the OpenCGA connection and login
con <- initOpencgaR(host = "http://localhost:8080/opencga/", version = "v1")
con <- opencgaLogin(opencga = con, userid = "user", passwd = "pass")

The package implements at least one function for each available resource (user, project, study, etc.). The list of functions are defined in R/AllGeneric.R. Currently, the following functions are available:

OpenCGA R functions
userClient(OpencgaR, user, action, params=NULL)
userConfigClient(OpencgaR, user, name, action, params=NULL)
userFilterClient(OpencgaR, user, name, action, params=NULL)
projectClient(OpencgaR, project, action, params=NULL)

studyClient(OpencgaR, study, action, params=NULL)
studyGroupClient(OpencgaR, study, group=NULL, action, params=NULL)
studyAclClient(OpencgaR, study, memberId, action, params=NULL)
studyVariablesetClient(OpencgaR, variableSet, action, params=NULL)
studyVariablesetFieldClient(OpencgaR, variableSet, action, params=NULL)

fileClient(OpencgaR, f, action, params=NULL)
fileAclClient(OpencgaR, f, memberId, action, params=NULL)

jobClient(OpencgaR, jobId, action, params=NULL)
jobAclClient(OpencgaR, jobId, memberId, action, params=NULL)

familyClient(OpencgaR, family, action, params=NULL)
familyAnnotationsetClient(OpencgaR, family, annotationsetName, action, params=NULL)
familyAclClient(OpencgaR, memberIds, action, params=NULL)

individualClient(OpencgaR, individual, action, params=NULL)
individualAnnotationsetClient(OpencgaR, individual, annotationsetName, action, params=NULL)
individualAclClient(OpencgaR, memberIds, action, params=NULL)

sampleClient(OpencgaR, sample, action, params=NULL) 
sampleAnnotationsetClient(OpencgaR, sample, annotationsetName, action, params=NULL) 
sampleAclClient(OpencgaR, memberIds, action, params=NULL)

cohortClient(OpencgaR, cohort, action, params=NULL)
cohortAnnotationsetClient(OpencgaR, cohort, annotationsetName, action, params=NULL)
cohortAclClient(OpencgaR, memberIds, action, params=NULL)

clinicalClient(OpencgaR, clinicalAnalysis, action, params=NULL)

metaClient(OpencgaR, action, params=NULL)

analysisVariantClient(OpencgaR, action, params=NULL)

Design Principles


API


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