GDCprepare_clinic: Parsing clinical xml files

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

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.