mpraSetExample: Example data for the mpra package.
In mpra: Analyze massively parallel reporter assays

Description Usage Format Details Source References Examples

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.

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

An MPRASet.

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.

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.

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.