count_table-class: Object containing the count table matrices, their names and...

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Object containing the count table matrices, their names and descriptions that we generated by provided and by user functions. These are used to discover and infer signatures and exposures.

Description

Object containing the count table matrices, their names and descriptions that we generated by provided and by user functions. These are used to discover and infer signatures and exposures.

Slots

name

A name that describes the type of table (e.g. "SBS96")

count_table

An array of counts with samples as the columns and motifs as the rows

annotation

A data.frame of annotations with three columns used for plotting: motif, mutation, and context

features

Original features used to generate the count_table

type

The mutation type of each feature, in case we need to plot or model they differently

color_variable

The variable used for plotting colors, selected from the annotation slot

color_mapping

The mapping of the annotations chosen by color_variable to color values for plotting

description

A summary table of the result objects in result_list a list of lists. The nested lists created combined (rbind) tables, and the tables at the first list level are modelled independantly. Combined tables must be named. list("tableA", comboTable = list("tableC", "tableD"))

campbio/musicatk documentation built on July 14, 2024, 8:28 a.m.