R: Inconsistency between data from TCGAbiolinks and GDC (does TCGAbiolinks retrieve Legacy data by default?)

Question

[fr]

Hi!

I'm using R and TCGAbiolinks to retrieve data and clinical data from GDC. To do so I use the following:

library(TCGAbiolinks)
patientdownload<-function("TCGA-LIHC"){
  clinquery<-GDCquery(project = "TCGA-LIHC",data.category = "Clinical")
  GDCdownload(clinquery,chunks.per.download = 30)
  prepatientout<-GDCprepare_clinic(clinquery, clinical.info = "patient")

However, I am finding some iconsistencies between what I'm getting and what is in GDC. For instance, for subject with 'bcr_patient_barcode=TCGA-DD-AADB' I retrieve the following data from 'GDCquery'

    bcr_patient_barcode gender  race_list   vital_status    neoplasm_histologic_grade   stage_event_pathologic_stage
18  TCGA-DD-AADF    FEMALE  ASIAN   Dead    G4  Stage I

However, when you look at the subject's data in GDC (here) everything is in agreement, with exception for Grade, which is never reported.

Why?

Could this mean that 'neoplasm_histologic_grade' is not the tumor grade? Or that 'GDCquery' is retrieving some Legacy data?

EDIT: this was now crossposted at github

Answer 1

[fr]

An answer to this question was added at the GitHub of TCGAbiolinks. Full credit goes to tiagochst (who is also here in biostars but I can't tag him).