This is an INCOMMON object resulting from the classification of all the example data.
Usage
data(MSK_PAAD_output)Examples
data(MSK_PAAD_output)
MSK_PAAD_output
#> ── [ INCOMMON ] 175054 PASS mutations across 24018 samples, with 290 mutant gen
#> ℹ Average sample purity: 0.4
#> ℹ Average sequencing depth: 649
#> # A tibble: 7,839 × 186
#> sample tumor_type purity chr from to ref alt NV DP gene
#> <chr> <chr> <dbl> <chr> <dbl> <dbl> <chr> <chr> <int> <int> <chr>
#> 1 P-0000142 PAAD 0.4 chr12 2.54e7 2.54e7 C C 273 1404 KRAS
#> 2 P-0000142 PAAD 0.4 chr17 7.58e6 7.58e6 G G 53 671 TP53
#> 3 P-0000142 PAAD 0.4 chr2 4.77e7 4.77e7 T T 31 481 MSH2
#> 4 P-0000142 PAAD 0.4 chr5 1.28e6 1.28e6 G G 34 227 TERT
#> 5 P-0000783 PAAD 0.8 chr12 2.54e7 2.54e7 C C 474 941 KRAS
#> 6 P-0000783 PAAD 0.8 chr5 1.12e8 1.12e8 G G 164 424 APC
#> 7 P-0000783 PAAD 0.8 chr11 8.60e7 8.60e7 T T 210 601 EED
#> 8 P-0000783 PAAD 0.8 chr13 3.29e7 3.29e7 TC TC 160 493 BRCA2
#> 9 P-0000879 PAAD 0.6 chr7 1.40e8 1.40e8 A A 308 736 BRAF
#> 10 P-0000879 PAAD 0.6 chr1 1.15e8 1.15e8 T T 188 506 NRAS
#> # ℹ 7,829 more rows
#> # ℹ 175 more variables: HGVSp_Short <chr>, Entrez_Gene_Id <dbl>, Center <chr>,
#> # NCBI_Build <chr>, Chromosome <chr>, Strand <chr>, Consequence <chr>,
#> # Variant_Classification <chr>, Variant_Type <chr>, Tumor_Seq_Allele2 <chr>,
#> # dbSNP_RS <chr>, dbSNP_Val_Status <lgl>, Matched_Norm_Sample_Barcode <lgl>,
#> # Match_Norm_Seq_Allele1 <lgl>, Match_Norm_Seq_Allele2 <lgl>,
#> # Tumor_Validation_Allele1 <lgl>, Tumor_Validation_Allele2 <lgl>, …