Data from the MSK-MetTropism cohort classified with INCOMMON

This is an INCOMMON object resulting from the classification of all the example data.

Usage

data(MSK_classified)

Format

An INCOMMON object with genomics, clinical data and classification results.

Source

"msk_classified_with_priors.rds" at Zenodo https://zenodo.org/records/10927218

Examples

data(MSK_classified)
MSK_classified
#> ── [ INCOMMON ]  176075 PASS mutations across 24117 samples, with 290 mutant gen
#> ℹ Average sample purity: 0.4
#> ℹ Average sequencing depth: 648
#> ── [ INCOMMON ]  Classified mutations with overdispersion parameter 0.01 and ent
#> ℹ There are: 
#> • N = 63649 mutations (HMD)
#> • N = 11905 mutations (LOH)
#> • N = 35087 mutations (CNLOH)
#> • N = 22803 mutations (AM)
#> • N = 42629 mutations (Tier-2)
#> # A tibble: 176,073 × 19
#>    sample    tumor_type purity chr     from     to ref   alt      DP    NV   VAF
#>    <chr>     <chr>       <dbl> <chr>  <dbl>  <dbl> <chr> <chr> <int> <int> <dbl>
#>  1 P-002891… CHOL          0.3 chr17 7.58e6 7.58e6 G     A       837   133 0.159
#>  2 P-002891… CHOL          0.3 chrX  5.32e7 5.32e7 G     A       832    85 0.102
#>  3 P-000369… BLCA          0.2 chr17 7.58e6 7.58e6 C     A       437   109 0.249
#>  4 P-000369… BLCA          0.2 chr5  1.49e8 1.49e8 C     T       360    36 0.1  
#>  5 P-000369… BLCA          0.2 chr13 3.29e7 3.29e7 G     C      1027   162 0.158
#>  6 P-000369… BLCA          0.2 chr13 3.29e7 3.29e7 G     C      1021   182 0.178
#>  7 P-000369… BLCA          0.2 chr19 1.11e7 1.11e7 G     T       573    98 0.171
#>  8 P-000369… BLCA          0.2 chr22 4.15e7 4.15e7 G     A       416    45 0.108
#>  9 P-000369… BLCA          0.2 chrX  4.49e7 4.49e7 C     T       730   194 0.266
#> 10 P-000382… BLCA          0.6 chr5  1.30e6 1.30e6 G     A       218   138 0.633
#> # ℹ 176,063 more rows
#> # ℹ 8 more variables: gene <chr>, HGVSp_Short <chr>, gene_role <chr>, id <chr>,
#> #   label <chr>, state <chr>, posterior <dbl>, entropy <dbl>