TCGA-SKCM

library(TCGAbiolinks)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

# XML files
query <- GDCquery(project = "TCGA-SKCM", 
                  data.category = "Clinical")
tryCatch(GDCdownload(query,files.per.chunk = 50))
stage <- GDCprepare_clinic(query, clinical.info = "stage_event")
load("stage.rda")

DT::datatable(stage,options = list(scrollX = TRUE),filter = 'top')

# Articles
curated_stages <- TCGAquery_subtype(tumor = "skcm") %>% dplyr::rename(., bcr_patient_barcode = patient)

## skcm subtype information from:doi:10.1016/j.cell.2015.05.044

DT::datatable(curated_stages[,c("bcr_patient_barcode","CURATED_PATHOLOGIC_STAGE_AJCC7_AT_DIAGNOSIS_SIMPLE","CURATED_PATHOLOGIC_STAGE_AJCC7_AT_DIAGNOSIS_COMPLEX")] 
,options = list(scrollX = TRUE),filter = 'top')

# GDC indexed
clinical <- GDCquery_clinic(project = "TCGA-SKCM", type = "clinical")
DT::datatable(clinical[c("submitter_id","tumor_stage")],options = list(scrollX = TRUE),filter = 'top')