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Retrieve variants from a musica object

Source: R/class_musica.R
variants.Rd

The variants data.table contains the variants and variant-level annotations

Usage

variants(object)

# S4 method for class 'musica'
variants(object)

variants(musica) <- value

# S4 method for class 'musica,data.table'
variants(musica) <- value

Arguments

object

A musica object generated by the create_musica_from_variants or create_musica_from_counts function.

musica

A musica object generated by the create_musica_from_variants or create_musica_from_counts 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
#>      <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