1 Introduction

The RaggedExperiment package provides a flexible data representation for copy number, mutation and other ragged array schema for genomic location data. It aims to provide a framework for a set of samples that have differing numbers of genomic ranges.

The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset. The row and column dimensions of the RaggedExperiment correspond to the number of ranges in the entire dataset and the number of samples represented in the data, respectively.

2 Installation

if (!require("BiocManager"))

Loading the package:


3 Citing RaggedExperiment

Your citations are crucial in keeping our software free and open source. To cite our package see the citation (Ramos et al. (2023)) in the Reference section. You may also browse to the publication at the link here.

4 RaggedExperiment class overview

A schematic showing the class geometry and supported transformations of the RaggedExperiment class is show below. There are three main operations for transforming the RaggedExperiment representation:

  1. sparseAssay
  2. compactAssay
  3. qreduceAssay