GDCprepare_clinic | 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",
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)
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