Subsets a variant table based on Variant Type

Usage

subset_variant_by_type(tab, type)

Arguments

tab: Input variant table
type: Variant type to return e.g. "SBS", "INS", "DEL", "DBS"

Value

Returns the input variant table subsetted to only contain variants of the specified variant type

Examples

data(musica)
annotate_variant_type(musica)
subset_variant_by_type(variants(musica), "SBS")
#>         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