## -------------------------------------------------------------------------- library("ExperimentHub") library("SummarizedExperiment") library("ggplot2") ## -------------------------------------------------------------------------- eh = ExperimentHub() query(eh, "CLLmethylation") meth = eh[["EH1071"]] # extract the methylation data ## -------------------------------------------------------------------------- methData = t(assay(meth)) #filter to only include top 5000 most variable sites ntop = 5000 methData = methData[,order(apply(methData, 2, var, na.rm=TRUE), decreasing=TRUE)[1:ntop]] ## -------------------------------------------------------------------------- # principal component analysis pcaMeth = prcomp(methData, center=TRUE, scale. = FALSE) ## -------------------------------------------------------------------------- summary(pcaMeth) ## -------------------------------------------------------------------------- tmp = data.frame(pcaMeth$x) ggplot(data=tmp, aes(x=PC1, y=PC2)) + geom_point() + theme_bw() ## -------------------------------------------------------------------------- sessionInfo()