CAGEr-class: CAGEr objects

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

The CAGEr package provides two classes of objects to load, contain and process CAGE data:

Details

• The CAGEset class is the original object format in CAGEr, as when published in Haberle et al., 2015.

• The CAGEexp class is a new class format in 2017, which is based on the MultiAssayExperiment class. In comparison with CAGEset, objects, CAGEexp objects benefit from a a more efficient data storage, using DataFrames of run-length-encoded (Rle) integers, allowing for the loading and use of much larger transcriptome datasets.

Most CAGEr functions support both classes interchangabely, and the CAGEr class was created for methods that support both classes identically.

References

Haberle V, Forrest ARR, Hayashizaki Y, Carninci P and Lenhard B (2015). “CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.” Nucleic Acids Research, 43, pp. e51., http://nar.oxfordjournals.org/content/43/8/e51

CAGEr documentation built on Jan. 17, 2021, 2 a.m.