GDCprepare_clinic {TCGAbiolinks} | R Documentation

## Parsing clinical xml files

### Description

This function receives the query argument and parses the clinical xml files based on the desired information

### Usage

    GDCprepare_clinic(query, clinical.info, directory = "GDCdata")

### Arguments

`query` | Result from GDCquery, with data.category set to Clinical
`clinical.info` | Which information should be retrieved. Options Clinical: drug, admin, follow_up,radiation, patient, stage_event or new_tumor_event Options Biospecimen: protocol, admin, aliquot, analyte, bio_patient, sample, portion, slide
`directory` | Directory/Folder where the data was downloaded. Default: GDCdata

### Value

A data frame with the parsed values from the XML

### Examples

    query <- GDCquery(project = "TCGA-COAD",
                      data.category = "Clinical",
                      file.type = "xml",
                      barcode = c("TCGA-RU-A8FL","TCGA-AA-3972"))
    GDCdownload(query)
    clinical <- GDCprepare_clinic(query,"patient")
    clinical.drug <- GDCprepare_clinic(query,"drug")
    clinical.radiation <- GDCprepare_clinic(query,"radiation")
    clinical.admin <- GDCprepare_clinic(query,"admin")
    query <- GDCquery(project = "TCGA-COAD",
                      data.category = "Biospecimen",
                       file.type = "xml",
                      data.type = "Biospecimen Supplement",
                      barcode = c("TCGA-RU-A8FL","TCGA-AA-3972"))
    GDCdownload(query)
    clinical <- GDCprepare_clinic(query,"admin")
    clinical.drug <- GDCprepare_clinic(query,"sample")
    clinical.radiation <- GDCprepare_clinic(query,"portion")
    clinical.admin <- GDCprepare_clinic(query,"slide")

[Package TCGAbiolinks version 2.22.4 Index]