Adds an annotation to the input musica's variant table with length of each variant

annotate_variant_length(musica)

Arguments

musica	Input samples

Value

None

Examples

data(musica)
annotate_variant_length(musica)
musica
#> An object of class "musica"
#> Slot "variants":
#>        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 Variant_Length
#>   1:          SBS              1
#>   2:          SBS              1
#>   3:          SBS              1
#>   4:          SBS              1
#>   5:          SBS              1
#>  ---                            
#> 907:          SBS              1
#> 908:          SBS              1
#> 909:          SBS              1
#> 910:          SBS              1
#> 911:          SBS              1
#> 
#> Slot "count_tables":
#> $SBS96
#> Count_Table:  SBS96 
#> Motifs: 96 
#> Samples: 7 
#>  
#> **Annotations: 
#>            motif mutation context
#> C>A_ACA C>A_ACA      C>A     ACA
#> C>A_ACC C>A_ACC      C>A     ACC
#> C>A_ACG C>A_ACG      C>A     ACG
#> C>A_ACT C>A_ACT      C>A     ACT
#> C>A_CCA C>A_CCA      C>A     CCA
#> C>A_CCC C>A_CCC      C>A     CCC
#> 7           ...      ...     ... 
#> 
#> **Features: 
#>    mutation
#> 1  C>A_TCA
#> 2  C>A_ACT
#> 3  T>C_ATT
#> 4  C>G_TCT
#> 5  T>G_CTC
#> 6  C>G_CCC
#> 7      ... 
#> 
#> **Types: 
#>  SBS
#>  
#> **Color Variable: 
#>  mutation
#>  
#> **Color Mapping: 
#>  #5ABCEBFF
#>  #050708FF
#>  #D33C32FF
#>  #CBCACBFF
#>  #ABCD72FF
#>  #E7C9C6FF
#>  
#> **Descriptions: 
#>  Single Base Substitution table with one base upstream and downstream
#> 
#> 
#> Slot "sample_annotations":
#>                         Samples Tumor_Subtypes
#> 1: TCGA-94-7557-01A-11D-2122-08           Lung
#> 2: TCGA-56-7582-01A-11D-2042-08           Lung
#> 3: TCGA-77-7335-01A-11D-2042-08           Lung
#> 4: TCGA-97-7938-01A-11D-2167-08           Lung
#> 5: TCGA-EE-A3J5-06A-11D-A20D-08         Breast
#> 6: TCGA-ER-A197-06A-32D-A197-08         Breast
#> 7: TCGA-ER-A19O-06A-11D-A197-08         Breast
#>