The count_tables contains standard and/or custom count tables created from variants

tables(object)

# S4 method for musica
tables(object)

# S4 method for musica_result
tables(object)

tables(musica) <- value

# S4 method for musica,list
tables(musica) <- value

Arguments

object

A musica object generated by the create_musica function or a musica_result object generated by a mutational discovery or prediction tool.

musica

A musica object generated by the create_musica function or a musica_result object generated by a mutational discovery or prediction tool.

value

A list of count_table objects representing counts of motifs in samples

Value

A list of count_tables

Examples

data(res) tables(res)
#> $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 #>
data(musica) tables(musica)
#> $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 #>