Hi everyone, 

I'm wondering how to retrieve the most accurate tumor stage at diagnosis information for the TCGA-SKCM dataset using TCGAbiolinks. I need stage information only in format stage I-IV. 

I retrieved the variable 'tumor_stage' as part of the indexed clinical data (using ‚GDCquery_clinic‘, see full reprex below). However, there is also a variable ‚CURATED_PATHOLOGIC_STAGE_AJCC7_AT_DIAGNOSIS_SIMPLE‘ as part of data provided by the original paper describing the TCGA-SKCM cohort (doi:10.1016/j.cell.2015.05.044), which TCGAbiolinks can pull using the query ‚TCGAquery_subtype‘. 

While these two variables largely concur there are some cases with a valid entry in the 'CURATED_PATHOLOGIC_STAGE_AJCC7_AT_DIAGNOSIS_SIMPLE' and 'not reported'  in 'tumor_stage' (e.g., patient 'TCGA-D9-A148'). Should I generate a new variable combining these two or is there a specific reason for this happening? 

Thanks very much,
Ben

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

## Download indexed clinical data
clinical <- GDCquery_clinic(project = "TCGA-SKCM", type = "clinical")

## Download curated stage information
curated_stages <- TCGAquery_subtype(tumor = "skcm") %>% dplyr::rename(., bcr_patient_barcode = patient)
#> skcm subtype information from:doi:10.1016/j.cell.2015.05.044

## join clinical data from GDCquery_clinic and TCGAquery_subtype retrievals
clinical_joined <- left_join(clinical, curated_stages, by = "bcr_patient_barcode") %>% 
  dplyr::select(bcr_patient_barcode, CURATED_PATHOLOGIC_STAGE_AJCC7_AT_DIAGNOSIS_SIMPLE, 
    tumor_stage)

## show specific case with non-matching entries
clinical_joined[clinical_joined$bcr_patient_barcode == "TCGA-D9-A148", ]
#>     bcr_patient_barcode CURATED_PATHOLOGIC_STAGE_AJCC7_AT_DIAGNOSIS_SIMPLE
#> 102        TCGA-D9-A148                                           Stage IV
#>      tumor_stage
#> 102 not reported

sessionInfo()
#> R version 3.4.4 (2018-03-15)
#> Platform: x86_64-apple-darwin15.6.0 (64-bit)
#> Running under: macOS High Sierra 10.13.4
#> 
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] dplyr_0.7.4         TCGAbiolinks_2.6.12
#> 
#> loaded via a namespace (and not attached):
#>   [1] colorspace_1.3-2            selectr_0.4-0              
#>   [3] rjson_0.2.15                hwriter_1.3.2              
#>   [5] rprojroot_1.3-2             circlize_0.4.3             
#>   [7] XVector_0.18.0              GenomicRanges_1.30.3       
#>   [9] GlobalOptions_0.0.13        ggpubr_0.1.6               
#>  [11] matlab_1.0.2                ggrepel_0.7.0              
#>  [13] bit64_0.9-7                 AnnotationDbi_1.40.0       
#>  [15] xml2_1.2.0                  codetools_0.2-15           
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