dbnp.test.R

## Test script to get NutriTech data from dbNP
## Crashes with:
## > source('~/projects/nutritech/code/dbnp.test.R')
## Clinical Chemistry
## Questionnaire Physical Activity
## Error in x$name : $ operator is invalid for atomic vectors

require(GSCFClient)
require(GSCFRUtils)

## Fill out your own dbNP user / pass here
user = "XXXX"
pass = "****"
token = "YYYY"
authenticate(user, pass, token)

studies = getStudies()

studyName = "NutriTechHIS"

study = studies[[grep(studyName, sapply(studies, function(x) x$code))]]
studyToken = study['token']

studyAssays = namedListToDataFrame(getAssaysForStudy(studyToken),"name")

assayData = list()
for(assayName in names(studyAssays)) {
  message(assayName)
  assayToken = studyAssays[[assayName]][2]
  assayData[[assayName]] = assayDataAsMatrix(assayToken)$data
}

subjects = getSubjectsForStudy(studyToken)