TCGA XML vs indexed

Download data

library(TCGAbiolinks)
library(dplyr)

clinical.indexed <- GDCquery_clinic(
    project = "TCGA-BRCA", 
    type = "clinical"
)

query.biotab <- GDCquery(
    project = "TCGA-BRCA", 
    data.category = "Clinical",
    data.type = "Clinical Supplement", 
    data.format = "BCR Biotab")
GDCdownload(query.biotab)
clinical.BCRtab.all <- GDCprepare(query.biotab)

query.xml <- GDCquery(
    project = "TCGA-COAD", 
    data.category = "Clinical", 
    file.type = "xml"
)
GDCdownload(query.xml)
clinical.xml.new_tumor <- GDCprepare_clinic(
    query.xml, 
    clinical.info = "new_tumor_event"
)

## Warning: `funs()` is deprecated as of dplyr 0.8.0.
## Please use a list of either functions or lambdas: 
## 
##   # Simple named list: 
##   list(mean = mean, median = median)
## 
##   # Auto named with `tibble::lst()`: 
##   tibble::lst(mean, median)
## 
##   # Using lambdas
##   list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.

Check XML file

table(clinical.BCRtab.all$clinical_patient_brca$new_tumor_event_dx_indicator)

## 
##                         [Not Available]                               [Unknown] 
##                                     891                                      11 
##                          CDE_ID:3121376 new_tumor_event_after_initial_treatment 
##                                       1                                       1 
##                                      NO                                     YES 
##                                     185                                      10

clinical.xml.new_tumor$bcr_patient_barcode %>% unique %>% length

## [1] 91