build_standard_table {musicatk} | R Documentation

## Builds count tables using various mutation type schemas

### Description

Generates count tables for different mutation type schemas which can be used as input to the mutational signature discovery or prediction functions. `"SBS96"` generates a table for single base substitutions following the standard 96 mutation types derived from the trinucleotide context. `"SBS192"` is the 96 mutation type schema with the addition of transcriptional strand or replication strand information added to each base. `"DBS"` generates a table for the double base substitution schema used in COSMIC V3. `"Indel"` generates a table for insertions and deletions following the schema used in COSMIC V3.

### Usage

    build_standard_table(
      musica,
      g,
      table_name,
      strand_type = NULL,
      overwrite = FALSE,
      verbose = FALSE
    )

### Arguments

`musica` | A `musica` object.
`g` | A BSgenome object indicating which genome reference the variants and their coordinates were derived from.
`table_name` | Name of standard table to build. One of `"SBS96"`, `"SBS192"`, `"DBS"`, or `"Indel"`.
`strand_type` | Strand type to use in SBS192 schema. One of `"Transcript_Strand"` or `"Replication_Strand"`. Only used if `table_name = SBS192`.
`overwrite` | If `TRUE`, any existing count table with the same name will be overwritten. If `FALSE`, then an error will be thrown if a table with the same name exists within the `musica` object.
`verbose` | Show progress bar for processed samples

### Value

No object will be returned. The count tables will be automatically added to the `musica` object.

### Examples

    g <- select_genome("19")

    data(musica)
    build_standard_table(musica, g, "SBS96", overwrite = TRUE)

    data(musica)
    annotate_transcript_strand(musica, "19")
    build_standard_table(musica, g, "SBS192", "Transcript_Strand")

    data(musica)
    data(rep_range)
    annotate_replication_strand(musica, rep_range)
    build_standard_table(musica, g, "SBS192", "Replication_Strand")

    data(dbs_musica)
    build_standard_table(dbs_musica, g, "DBS", overwrite = TRUE)

    data(indel_musica)
    build_standard_table(indel_musica, g, table_name = "INDEL")

[Package musicatk version 1.2.0 Index]