Adds an annotation to the input musica's variant table with length of each variant
Source:R/annotate_variants.R
annotate_variant_length.RdAdds an annotation to the input musica's variant table with length of each variant
Examples
data(musica)
annotate_variant_length(musica)
musica
#> An object of class "musica"
#> Slot "variants":
#> 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
#> ---
#> 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
#> <char> <num>
#> 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
#>
#> Slot "result_list":
#> List of length 0
#>