The variants data.table contains the variants
and variant-level annotations
variants(object)
# S4 method for musica
variants(object)
# S4 method for musica_result
variants(object)
variants(musica) <- value
# S4 method for musica,data.table
variants(musica) <- valueA musica object generated by
the create_musica function or a musica_result
object generated by a mutational discovery or prediction tool.
A musica object generated by
the create_musica function
A data.table of mutational variants and
variant-level annotations
A data.table of variants
data(res)
variants(res)
#> chr start end ref alt sample
#> <fctr> <num> <num> <char> <char> <fctr>
#> 1: chr1 11020563 11020563 C A TCGA-94-7557-01A-11D-2122-08
#> 2: chr1 43430030 43430030 G T TCGA-94-7557-01A-11D-2122-08
#> 3: chr1 58682403 58682403 A G TCGA-94-7557-01A-11D-2122-08
#> 4: chr1 109508295 109508295 C G TCGA-94-7557-01A-11D-2122-08
#> 5: chr1 156384826 156384826 A C TCGA-94-7557-01A-11D-2122-08
#> ---
#> 880: chr19 54885292 54885292 G A TCGA-ER-A19O-06A-11D-A197-08
#> 881: chr20 49374328 49374328 A T TCGA-ER-A19O-06A-11D-A197-08
#> 882: chrX 73213768 73213768 T G TCGA-ER-A19O-06A-11D-A197-08
#> 883: chrX 101292834 101292834 G A TCGA-ER-A19O-06A-11D-A197-08
#> 884: chrX 107526690 107526690 C T TCGA-ER-A19O-06A-11D-A197-08
#> Variant_Type
#> <char>
#> 1: SBS
#> 2: SBS
#> 3: SBS
#> 4: SBS
#> 5: SBS
#> ---
#> 880: SBS
#> 881: SBS
#> 882: SBS
#> 883: SBS
#> 884: SBS
data(musica)
variants(musica)
#> chr start end ref alt sample
#> <fctr> <num> <num> <char> <char> <fctr>
#> 1: chr1 11020563 11020563 C A TCGA-94-7557-01A-11D-2122-08
#> 2: chr1 43430030 43430030 G T TCGA-94-7557-01A-11D-2122-08
#> 3: chr1 58682403 58682403 A G TCGA-94-7557-01A-11D-2122-08
#> 4: chr1 109508295 109508295 C G TCGA-94-7557-01A-11D-2122-08
#> 5: chr1 156384826 156384826 A C TCGA-94-7557-01A-11D-2122-08
#> ---
#> 907: chr19 54885292 54885292 G A TCGA-ER-A19O-06A-11D-A197-08
#> 908: chr20 49374328 49374328 A T TCGA-ER-A19O-06A-11D-A197-08
#> 909: chrX 73213768 73213768 T G TCGA-ER-A19O-06A-11D-A197-08
#> 910: chrX 101292834 101292834 G A TCGA-ER-A19O-06A-11D-A197-08
#> 911: chrX 107526690 107526690 C T TCGA-ER-A19O-06A-11D-A197-08
#> Variant_Type
#> <char>
#> 1: SBS
#> 2: SBS
#> 3: SBS
#> 4: SBS
#> 5: SBS
#> ---
#> 907: SBS
#> 908: SBS
#> 909: SBS
#> 910: SBS
#> 911: SBS