JKscience_TS2A: Table S2A for cis-eQTLs among shared datasets from Benjamin...

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

This dataset involves 228 individuals with expression data for all four conditions, that is, in the naive state (Naive), after 2-hour LPS (LPS2), after 24-hour LPS (LPS24), and after exposure to IFN (IFN). Local, likely cis-acting eQTL (referred to as cis-eQTL) were defined as SNPs showing association with gene expression that were located within a 1-Mb window of the associated probe. The eQTL analysis was performed with the R package MatrixEQTL using an additive linear model, reporting both test statistic and FDR.

Usage

data(JKscience_TS2A)

Value

a data frame. It has the following columns: "variant" (cis-eQTLs), "ArrayAddress" (illuminaHumanv4), "GeneID" (Entrez GeneID), "Symbol" (gene symbol), "Naive_t" (test statistic for naive samples), "LPS2_t", "LPS24_t", "IFN_t", "Naive_fdr" (FDR for naive samples), "LPS2_fdr", "LPS24_fdr" and "IFN_fdr".

References

Fairfax et al. (2014). Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science, 343(6175):1246949.

Examples

## Not run: 
JKscience_TS2A <- xRDataLoader(RData.customised='JKscience_TS2A')
JKscience_TS2A[1:5,]

## End(Not run)

XGR documentation built on June 18, 2019, 3:01 p.m.