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

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

Table S2A for cis-eQTLs among shared datasets from Benjamin et al. (2014)

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)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.