The musica musica contains variants,
count tables, and sample annotations
get_musica(result)
# S4 method for musica_result
get_musica(result)A musica_result object generated by
a mutational discovery or prediction tool.
A musica musica object
data(res)
get_musica(res)
#> 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
#> ---
#> 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
#>
#> 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":
#> Null data.table (0 rows and 0 cols)
#>