CAGEr-class {CAGEr} | R Documentation

## CAGEr objects

### 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 `DataFrame`s 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

[Package CAGEr version 1.30.3 Index]