# #设置,包括= FALSE ----------------------------------------------------- 美元knitr: opts_chunk集(消息= FALSE,警告= FALSE) # #——Load_Packages,消息= FALSE ------------------------------------------- 库(餐)库(brgedata)图书馆(MultiDataSet)图书馆(missMethyl)图书馆(minfi)图书馆(GenomicRanges)库(ggplot2) # #——Methylation_Data --------------------------------------------------------- 数据(brge_methy) brge_methy colData (brge_methy) # #——Expression_Data ---------------------------------------------------------- 数据(brge_gexp) brge_gexp lapp (pData (brge_gexp),表 ) ## ----------------------------------------------------------------------------- targetRange < -农庄(“chr11:102600000 - 103300000 ") ## ---- Meth_Analysis ------------------------------------------------------------ cellCounts < - colnames (colData (brge_methy) [3:9] methRes < - runDiffMeanAnalysis (= = brge_methy,模型公式(粘贴(“~性+”,粘贴(cellCounts,崩溃 = "+")))) methRes名称(methRes) # #——情节QQ 1 ---------------------------------------------------------------- 情节(methRes掉= " DiffMean ", qq type = " ") ## ---- 曼哈顿 --------------------------------------------------------------- targetRangeNum < -农庄(“11:102600000 - 103300000”)的阴谋(methRes掉=“DiffMean类型=“曼哈顿”,主要=“不同的手段”,突出= targetRangeNum) # #——实验显示 ----------------------------------------------------------------- targetRange < -农庄(chr11:102600000 - 103300000) gexpRes < - runDiffMeanAnalysis(集= brge_gexp模型= ~性)的名字(gexpRes) # #——情节QQ实验1 ------------------------------------------------------------ 情节(gexpRes掉= " DiffMean ", qq type = " ") ## ---- 肿瘤基因火山 ------------------------------------------------------------- 情节(gexpRes掉= " DiffMean ",类型=“火山”)+ ggtitle(“不同的意思 ") ## ---- 曼哈顿肝 ---------------------------------------------------------- targetRange < -农庄(chr11:102600000 - 103300000)情节(gexpRes掉=“DiffMean”类型=“曼哈顿”,主要=“不同的手段”,强调= targetRangeNum) # #——区域图2实验 ------------------------------------------------------ plotRegion(资源集= methRes rset2 = gexpRes,范围= targetRange) # #——新多冰毒Exp ------------------------------------------------------- 多< - createMultiDataSet()多< - add_genexp(多,brge_gexp)多< - add_methy(多,brge_methy ) ## ----------------------------------------------------------------------------- 多。filt < -多(,targetRange) # #——Corr冰毒Exp ------------------------------------------------------------ methExprs < - correlationMethExprs (multi.filt)头(methExprs) # #——SessionInfo -------------------------------------------------------------- sessionInfo ()