A data frame containing clinical and pathological annotations for the
TCGA stomach adenocarcinoma (STAD) cohort. Each row corresponds to one
tumour sample and can be matched to the columns of eset_stad via
the ID column. This dataset is typically used together with
eset_stad in examples of survival analysis, subgroup comparison
and immune deconvolution in the IOBR package.
Usage
data(pdata_stad)Format
A data frame with one row per TCGA-STAD sample and 8 variables:
- ID
Character. TCGA sample barcode, matching the column names of
eset_stad.- stage
Factor. Pathological stage (e.g.
"Stage_I","Stage_II","Stage_III","Stage_IV").- status
Factor. Vital status at last follow-up (
"Alive"or"Dead").- Lauren
Factor. Lauren classification of gastric cancer (
"Intestinal","Diffuse","Mixed"orNA).- subtype
Factor. Molecular subtype (e.g.
"CIN","EBV","GS","MSI").- EBV
Factor. EBV status of the tumour (
"Positive"or"Negative").- time
Numeric. Overall survival or follow-up time, typically measured in months.
- OS_status
Integer/binary. Overall survival status indicator. (
1= death,0= censored)
Examples
data(pdata_stad)
head(pdata_stad)
#> ID stage status Lauren subtype EBV time OS_status
#> 61 TCGA-BR-8365 Stage_II Dead Mixed CIN Negitive 17.77 1
#> 58 TCGA-BR-8297 Stage_III Alive Diffuse CIN Negitive 7.50 0
#> 23 TCGA-BR-6564 Stage_III Dead Diffuse CIN Negitive 26.47 1
#> 65 TCGA-BR-8369 Stage_III Alive Mixed CIN Negitive 14.23 0
#> 87 TCGA-BR-8682 Stage_II Alive Intestinal CIN Negitive 33.03 0
#> 125 TCGA-CD-A489 Stage_II Dead Diffuse CIN Negitive 11.47 1