Subsets a variant table based on Variant Type

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
#>   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