R: Get clinical data for cancer study

cgdsr-getClinicalData {cgdsr} | R Documentation

## Get clinical data for cancer study

### Description

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

### Usage

    ## S3 method for class '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.

### Author(s)

<jacobsen@cbio.mskcc.org>

### References

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

### See Also

`cgdsr`,`CGDS`,`getCaseLists`

### Examples

    # 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)

[Package cgdsr version 1.2.10 Index]