mpraSetExample {mpra} | R Documentation

## Example data for the mpra package.

### Description

Example data for the MPRA package. `mpraSetExample` and `mpraSetAggExample` come from a study by Inoue et al that compares episomal and lentiviral MPRA. The former contains data at the barcode level and the latter contains data aggregated over barcodes. `mpraSetAllelicExample` come from a study by Tewhey et al that looks at regulatory activity of allelic versions of thousands of SNPs to follow up on prior eQTL results.

### Usage

    data("mpraSetExample")
    data("mpraSetAggExample")
    data("mpraSetAllelicExample")

### Format

An `MPRASet`.

### Details

`mpraSetExample` contains barcode level information for the study by Inoue et al. `mpraSetAggExample` contains count information from `mpraSetExample` where the counts have been summed over barcodes for each element. `mpraSetAllelicExample` contains count information for the Tewhey et al study. The counts have been summed over barcodes for each element.

### Source

A script for creating the three datasets is supplied in the `scripts` folder of the package. The data are taken from the GEO submission associated with the paper (see references), specifically GSE83894 and GSE75661.

### References

Inoue, Fumitaka, Martin Kircher, Beth Martin, Gregory M. Cooper, Daniela M. Witten, Michael T. McManus, Nadav Ahituv, and Jay Shendure. A Systematic Comparison Reveals Substantial Differences in Chromosomal versus Episomal Encoding of Enhancer Activity. Genome Research 2017, 27(1):38-52. doi: 10.1101/gr.212092.116.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC. Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. Cell 2016, 165:1519-1529. doi: 10.1016/j.cell.2016.04.027.

### Examples

    data(mpraSetAggExample)

[Package mpra version 1.14.0 Index]