Object construction

Introduction

The riboTransVis package provides support for constructing two core S4 object types: ribotrans and serp.

The ribotrans object is designed for standard ribosome profiling (Ribo-seq) data analysis. It encapsulates common inputs such as read coverage, transcript features, and annotation metadata, enabling downstream analyses like occupancy profiling, differential translation, and transcript-level visualization.

The serp object extends this functionality for analyzing selective ribosome profiling (selective Ribo-seq) experiments, which are often used to investigate specialized ribosome populations (e.g., via immunoprecipitation). In addition to inheriting all slots and methods from ribotrans, the serp class introduces additional slots for IP and total RNA signals, enrichment ratios, and specialized metadata structures.

Because serp is derived from ribotrans, many methods implemented for ribotrans objects are also compatible with serp objects, ensuring a consistent and modular workflow across both conventional and selective Ribo-seq data types.

Together, these two object classes provide a flexible and extensible structure for managing and analyzing diverse Ribo-seq datasets in an efficient and scalable manner.