The musica musica contains variants,
count tables, and sample annotations
get_musica(result) # S4 method for musica_result get_musica(result)
| result | A |
|---|
A musica musica object
data(res) get_musica(res) #> 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 #> --- #> 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 #> #> 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) #>