This dataset involves 228 individuals with genotype data. These individuals also contain expression data for all four conditions/contexts; see JKscience_expression. Also included are the SNP information and the demographics information about individuals.
JKscience_genotype <- dRDataLoader(RData.customised = "JKscience_genotype")
a list with 3 components:
sGenotype: an object of the dgCMatrix class (a sparse matrix of SNP X individuals). The possible values are '0' (carrying both major alleles), '1' (carrying heterogeneous alleles, one major allele and one minor allele), '2' (carrying both minor alleles), and 'NA' (missing data)
snpInfo: a list of 2 components, both storing SNP information including their genomic locations. The component JKscience_genotype$snpInfo$Info contains a data frame, the second JKscience_genotype$snpInfo$GR is an object of class "GRanges"
demoInfo: a data frame containing demographics information about individuals
Fairfax et al. (2014). Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science, 343(6175):1246949.
JKscience_genotype <- dRDataLoader(RData.customised='JKscience_genotype')Error in dRDataLoader(RData.customised = "JKscience_genotype"): unused argument (RData.customised = "JKscience_genotype")names(JKscience_genotype)Error in eval(expr, envir, enclos): object 'JKscience_genotype' not found# for sGenotype dim(JKscience_genotype$sGenotype)Error in eval(expr, envir, enclos): object 'JKscience_genotype' not foundJKscience_genotype$sGenotype[1:5, 1:5]Error in eval(expr, envir, enclos): object 'JKscience_genotype' not found# for snpInfo names(JKscience_genotype$snpInfo)Error in eval(expr, envir, enclos): object 'JKscience_genotype' not foundJKscience_genotype$snpInfo$Info[1:5, ]Error in eval(expr, envir, enclos): object 'JKscience_genotype' not foundJKscience_genotype$snpInfo$GRError in eval(expr, envir, enclos): object 'JKscience_genotype' not found# for demoInfo JKscience_genotype$demoInfo[1:5, ]Error in eval(expr, envir, enclos): object 'JKscience_genotype' not found