GDCprepare_clinic: Parsing clinical xml files

GDCprepare_clinicR 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",
  data.format = "bcr 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")
## Not run: 
query <- GDCquery(
   project = "TCGA-COAD",
   data.category = "Biospecimen",
   data.format = "bcr 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")

## End(Not run)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.