GDCprepare_clinic {TCGAbiolinks} | R Documentation |
This function receives the query argument and parses the clinical xml files based on the desired information
GDCprepare_clinic(query, clinical.info, directory = "GDCdata")
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 |
A data frame with the parsed values from the XML
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")