BRCA ER status

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

# All available tables
names(clinical.BCRtab.all)

## [1] "clinical_follow_up_v4.0_brca"     "clinical_follow_up_v2.1_brca"    
## [3] "clinical_drug_brca"               "clinical_follow_up_v4.0_nte_brca"
## [5] "clinical_follow_up_v1.5_brca"     "clinical_omf_v4.0_brca"          
## [7] "clinical_radiation_brca"          "clinical_nte_brca"               
## [9] "clinical_patient_brca"

# colnames from clinical_patient_brca
tibble::tibble(sort(colnames(clinical.BCRtab.all$clinical_patient_brca)))

# ER status count
plyr::count(clinical.BCRtab.all$clinical_patient_brca$er_status_by_ihc)

# ER content 
DT::datatable(clinical.BCRtab.all$clinical_patient_brca[,c(2,grep("^er",colnames(clinical.BCRtab.all$clinical_patient_brca)))])

# All columns content first rows
DT::datatable(head(clinical.BCRtab.all$clinical_patient_brca))