cgdsr (version 1.3.0)

cgdsr-getClinicalData: Get clinical data for cancer study

Description

Queries the CGDS API and returns clinical data for a given case list.

Usage

# S3 method for CGDS
getClinicalData(x, caseList, cases, caseIdsKey, ...)

Arguments

x

A CGDS object (required)

caseList

A case list ID

cases

A vector of case IDs

caseIdsKey

Only used by web portal.

...

Not used.

Value

A data.frame with rows for each case, rownames corresponding to case IDs, and columns:

1. overall_survival_months: Overall survival, in months.

2. overall_survival_status: Overall survival status, usually indicated as "LIVING" or "DECEASED".

3. disease_free_survival_months: Disease free survival, in months.

4. disease_free_survival_status: Disease free survival status, usually indicated as "DiseaseFree" or "Recurred/Progressed".

5. age_at_diagnosis: Age at diagnosis.

References

cBio Cancer Genomics Portal: http://www.cbioportal.org/

See Also

cgdsr,CGDS,getCaseLists

Examples

# NOT RUN {
# Create CGDS object
mycgds = CGDS("http://www.cbioportal.org/")

getCancerStudies(mycgds)

# Get available case lists (collection of samples) for a given cancer study 
mycancerstudy = getCancerStudies(mycgds)[2,1]
mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]

# Get clinical data for caselist
getClinicalData(mycgds,mycaselist)

# }