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tiagochst/clinical.R Secret

Created August 30, 2016 18:20
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explaining clinical data
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clinical.R
clin.query <- GDCquery(project = "TCGA-BLCA",
data.category = "Clinical")
GDCdownload(clin.query)
clinical.patient <- GDCprepare_clinic(clin.query, clinical.info = "patient")
clinical.patient.followup <- GDCprepare_clinic(clin.query, clinical.info = "follow_up")
clinical.index <- GDCquery_clinic("TCGA-BLCA")
# verify
> clinical.patient[grepl("a5c0",clinical.patient$patient_id, ignore.case = T),c("vital_status","days_to_death","days_to_last_followup")]
vital_status days_to_death days_to_last_followup
60 Alive 209
> clinical.patient.followup[grepl("a5c0",clinical.patient.followup$bcr_followup_barcode, ignore.case = T),c("vital_status","days_to_death","days_to_last_followup")]
vital_status days_to_death days_to_last_followup
61 Alive 407
62 Dead 550
> clinical.index[grepl("a5c0",clinical.index$submitter_id, ignore.case = T),c("vital_status","days_to_death","days_to_last_follow_up")]
vital_status days_to_death days_to_last_follow_up
197 dead 550 407
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