thehyve/GSCF-RClient

Name: GSCF-RClient

Owner: The Hyve

Description: R client to connect to GSCF

Created: 2012-08-02 08:34:01.0

Updated: 2013-01-11 13:35:49.0

Pushed: 2012-08-02 09:17:23.0

Homepage: null

Size: 107

Language: R

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

R2GSCF

An R client to connect to GSCF.

How to install

Download the package file from github: https://github.com/thomaskelder/R2GSCF/blob/master/GSCFClient_1.0.tar.gz

And install it in R:

all.packages('/path/to/GSCFClient_1.0.tar.gz', repo=NULL)

How to use

Below is a simple manual on how to use this R client. For a more complete example, please see this script.

Load the R client package:

ary(GSCFClient)

Or. if you prefer to load the library without installing, you can also run it directly from source:

ary(devtools)
ce_url("https://raw.github.com/PhenotypeFoundation/GSCF-RClient/master/dbnp.functions.R")

Specify to which instance of GSCF you wish to connect:

scfBaseUrl("http://old.studies.dbnp.org/api/")

Specify your authentication information and login to GSCF. You can lookup your shared key on the GSCF website, under user -> profile. Do not forget to ask an admin to give you ROLE_CLIENT privileges.

 = "yourUsername"
 = "yourPass"
 = "yourSharedKey"
enticate(user, pass, skey)

Now you can call the GSCF API functions in your R script, e.g.:

et available studies
ies = getStudies()

ook for the NuGO PPS2 study
y = studies[[grep("PPS2", sapply(studies, function(x) x$title))]]
yToken = study['token']

et the subject information for the study
ects = getSubjectsForStudy(studyToken)

et some assay data for the study
ys = getAssaysForStudy(studyToken)
yNames = sapply(assays, function(x) x$name)
ssay = names(assayNames[grep("chemistry", assayNames)])
ata = assayDataAsMatrix(samAssay)

t(samData$data[1:3,c("sampleToken", "measurement", "value")])
his will give:
                         sampleToken measurement value
 a9756533-108c-43d4-b1e0-d82d6a7d0781 adiponectin  8.64
 a9756533-108c-43d4-b1e0-d82d6a7d0781 Cholesterol 3.182
 8ac44d05-8203-4171-85f4-f81e78399d6a Cholesterol  4.49