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TCGA-STAD Clinical and Molecular Annotation Data

Source: R/data_doc.R
tcga_stad_pdata.Rd

Clinical, molecular, and signature score data for TCGA stomach adenocarcinoma (STAD) samples. Includes patient demographics, tumor characteristics, molecular subtypes, and pre-computed signature scores.

Usage

data(tcga_stad_pdata)

Format

A data frame with samples as rows and variables as columns:

  • ID – TCGA sample barcode

  • stage – tumor stage (Stage_I, Stage_II, etc.)

  • status – vital status (Alive/Dead)

  • Lauren – histological classification

  • subtype – molecular subtype (EBV, MSI, GS, CN, ...)

  • EBV – EBV infection status

  • TMEscore_plus – continuous tumor-micro-environment score

  • TMEscore_plus_binary – High/Low TME classification

  • time – follow-up time (months)

  • OS_status – 0 = alive, 1 = dead

  • ARID1A, PIK3CA – driver-gene mutation status

  • MALAT1 – lncRNA expression

  • remaining columns – gene-expression values and additional clinical/molecular annotations

Source

The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD)

References

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513, 202-209 (2014). doi:10.1038/nature13480

Examples

data(tcga_stad_pdata)
head(tcga_stad_pdata)
#> # A tibble: 6 × 17
#>   ID        stage status Lauren subtype EBV   TMEscore_plus TMEscore_plus_binary
#>   <fct>     <fct> <fct>  <fct>  <fct>   <chr>         <dbl> <fct>               
#> 1 TCGA-3M-… Stag… Alive  Mixed  NA      NE           0.0874 Low                 
#> 2 TCGA-B7-… Stag… Alive  Diffu… EBV     Posi…        2.03   High                
#> 3 TCGA-B7-… Stag… Alive  Diffu… NA      NE          -0.0423 Low                 
#> 4 TCGA-B7-… Stag… Alive  Intes… NA      NE          -0.686  Low                 
#> 5 TCGA-B7-… Stag… Alive  Intes… NA      NE           2.51   High                
#> 6 TCGA-B7-… Stag… Alive  Mixed  NA      NE          -0.627  Low                 
#> # ℹ 9 more variables: time <dbl>, OS_status <int>, ARID1A <chr>, PIK3CA <chr>,
#> #   MALAT1 <dbl>, GZMB <dbl>, GNLY <dbl>, CD274 <dbl>, HOTAIR <dbl>