Retrieve variants from a musica or musica_result object

Source: R/methods.R

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