regionAssoc: Associations between regulatory regions and expressed genes

In AffiXcan: A Functional Approach To Impute Genetically Regulated Expression

Description

Toy data used in examples to describe affiXcanTrain() and affiXcanImpute() functions.

Usage

data(regionAssoc)

Format

An object of class data.frame

Details

The object consists in a data.frame with two columns: for every "EXPRESSED_REGION" are listed the associated "REGULATORY_REGION"(s). For the illustrative purpose there are only two expressed genes: "ENSG00000139269.2" and "ENSG00000256377.1" (the same names are used in the SummarizedExperiment object containing the expression matrix, see help(exprMatrix) ).

For every gene, the associated regulatory regions were retrieved among the enhancers predicted by preSTIGE, a tool developed by O. Corradin et al. (https://genome.cshlp.org/content/24/1/1.full), in EBV-transformed lymphocytes cell lines. The name of the regulatory region being identical to the name of the expressed gene means that the regulatory region refers to a genomic window that spans at least for 2 Kbp and includes the most upstream TSS of the gene.

Examples

data(regionAssoc)
head(regionAssoc)

AffiXcan documentation built on Nov. 8, 2020, 8:07 p.m.