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) <- value

Arguments

object

A musica object generated by the create_musica function or a musica_result object generated by a mutational discovery or prediction tool.

musica

A musica object generated by the create_musica function

value

A data.table of mutational variants and variant-level annotations

Value

A data.table of variants

Examples

data(res) variants(res)
#> chr start end ref alt sample #> 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 #> 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 #> 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 #> 1: SBS #> 2: SBS #> 3: SBS #> 4: SBS #> 5: SBS #> --- #> 907: SBS #> 908: SBS #> 909: SBS #> 910: SBS #> 911: SBS