## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(message = FALSE, warning = FALSE) ## ----Load_Packages, message = FALSE------------------------------------------- library(MEAL) library(brgedata) library(MultiDataSet) library(missMethyl) library(minfi) library(GenomicRanges) library(ggplot2) ## ----Methylation_Data--------------------------------------------------------- data(brge_methy) brge_methy colData(brge_methy) ## ----Expression_Data---------------------------------------------------------- data(brge_gexp) brge_gexp lapply(pData(brge_gexp), table) ## ----------------------------------------------------------------------------- targetRange <- GRanges("chr11:102600000-103300000") ## ----Meth_Analysis------------------------------------------------------------ cellCounts <- colnames(colData(brge_methy))[3:9] methRes <- runDiffMeanAnalysis(set = brge_methy, model = formula(paste("~ sex +", paste(cellCounts, collapse = "+")))) methRes names(methRes) ## ----Plot QQ 1---------------------------------------------------------------- plot(methRes, rid = "DiffMean", type = "qq") ## ----Manhattans--------------------------------------------------------------- targetRangeNum <- GRanges("11:102600000-103300000") plot(methRes, rid = "DiffMean", type = "manhattan", main = "Differences in Means", highlight = targetRangeNum) ## ----Exp show----------------------------------------------------------------- targetRange <- GRanges("chr11:102600000-103300000") gexpRes <- runDiffMeanAnalysis(set = brge_gexp, model = ~ sex) names(gexpRes) ## ----Plot QQ exp 1------------------------------------------------------------ plot(gexpRes, rid = "DiffMean", type = "qq") ## ----Volcano gexp------------------------------------------------------------- plot(gexpRes, rid = "DiffMean", type = "volcano") + ggtitle("Differences in Means") ## ----Manhattans gexp---------------------------------------------------------- targetRange <- GRanges("chr11:102600000-103300000") plot(gexpRes, rid = "DiffMean", type = "manhattan", main = "Differences in Means", highlight = targetRangeNum) ## ----Regional plot 2 exp------------------------------------------------------ plotRegion(rset = methRes, rset2 = gexpRes, range = targetRange) ## ----New Multi Meth Exp------------------------------------------------------- multi <- createMultiDataSet() multi <- add_genexp(multi, brge_gexp) multi <- add_methy(multi, brge_methy) ## ----------------------------------------------------------------------------- multi.filt <- multi[, , targetRange] ## ----Corr Meth Exp------------------------------------------------------------ methExprs <- correlationMethExprs(multi.filt) head(methExprs) ## ----SessionInfo-------------------------------------------------------------- sessionInfo()