GDCprepare_clinic: Parsing clinical xml files

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

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")

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.