CAGEr-class {CAGEr}R Documentation

CAGEr objects

Description

The CAGEr package provides one classe of objects to load, contain and process CAGE data: the CAGEexp class, introduced 2017, which is based on the MultiAssayExperiment class. In comparison with the original CAGEset class (removed in 2021) 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.

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


[Package CAGEr version 2.0.2 Index]