R: Parsing clinical xml files

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",
                  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",
                  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 2.6.12 Index]