build_custom_table: Builds a custom table from specified user variants

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

Builds a custom table from specified user variants

Usage

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

Arguments

bay	Input samples
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 bagel 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 bagel's count_tables list and nothing is returned

Examples

bay <- readRDS(system.file("testdata", "bagel.rds", package = "BAGEL"))
annotate_transcript_strand(bay, "19", build_table = FALSE)
build_custom_table(bay, "Transcript_Strand", "Transcript_Strand",
data_factor = factor(c("T", "U")))

campbio/BAGEL documentation built on Oct. 6, 2020, 3:59 a.m.