Builds a custom table from specified user variants

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)
#>   403 genes were dropped because they have exons located on both strands
#>   of the same reference sequence or on more than one reference sequence,
#>   so cannot be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a
#>   GRangesList object, or use suppressMessages() to suppress this message.
build_custom_table(musica, "Transcript_Strand", "Transcript_Strand",
data_factor = factor(c("T", "U")))