build_custom_table {musicatk} | R Documentation

## Builds a custom table from specified user variants

### Description

Builds a custom table from specified user variants

### Usage

    build_custom_table(
      musica,
      variant_annotation,
      name,
      description = character(),
      data_factor = NA,
      annotation_df = NULL,
      features = NULL,
      type = NULL,
      color_variable = NULL,
      color_mapping = NULL,
      return_instead = FALSE,
      overwrite = FALSE
    )

### Arguments

`musica` | A `musica` object.
`variant_annotation` | User column to use for building table
`name` | Table name to refer to (must be unique)
`description` | Optional description of the table content
`data_factor` | Full set of table values, in case some are missing from the data. If NA, a superset of all available unique data values will be used
`annotation_df` | A data.frame of annotations to use for plotting
`features` | A data.frame of the input data from which the count table will be built
`type` | The type of data/mutation in each feature as an Rle object
`color_variable` | The name of the column of annotation_df used for the coloring in plots
`color_mapping` | The mapping from the values in the selected color_variable column to color values for plotting
`return_instead` | Instead of adding to musica object, return the created table
`overwrite` | Overwrite existing count table

### Value

If return_instead = TRUE then the created table object is returned, otherwise the table object is automatically added to the musica's count_tables list and nothing is returned

### Examples

    data(musica)
    annotate_transcript_strand(musica, "19", build_table = FALSE)
    build_custom_table(musica, "Transcript_Strand", "Transcript_Strand",
    data_factor = factor(c("T", "U")))

[Package musicatk version 1.2.0 Index]