This dataset involves the complete 432 individuals in 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.
JKscience_TS2B <- dRDataLoader(RData.customised = "JKscience_TS2B")
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".
Fairfax et al. (2014). Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science, 343(6175):1246949.
JKscience_TS2B <- dRDataLoader(RData.customised='JKscience_TS2B')Error in dRDataLoader(RData.customised = "JKscience_TS2B"): unused argument (RData.customised = "JKscience_TS2B")JKscience_TS2B[1:5,]Error in eval(expr, envir, enclos): object 'JKscience_TS2B' not found