## ----设置，包括= false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set(message = FALSE, warning = FALSE) ## ---- message = FALSE---------------------------------------------------------------------------------库（餐）图书馆（MultidataSet）库（MinFidata）库（MINFI）库（GGPLOT2）数据（“ MSETEX”）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------甲基<- Maptogenome（Ratioconvert（MSETEX））rowdata（meth）< - getAnnotation（meth）[，-c（1：3）] ##删除测量SNP的探针Meth <-DropmethylationLoci（Meth）##用SNP Meth <-DroplociwithSnps（Meth）##删除探针##使用nas meth <-Meth [！appl（getBeta（meth），1，函数（x）任何（is.na（x））），] ##选择样品的子集set.seed（0）meth（0）meth < - meth[示例（nrow（meth），100000），] ## ----管道，警告= false，eval = false ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃res <-runpipeline（set = meth，variable_names =“ status”）## ---- pipeline adj，警告= false ------------------------------------------------------------------------------------------------------------- runpipeline（set = meth，variable_names =“ status”，covariable_names =“ age”，分析= c（“ diffmean”，“ diffvar”））resadj ##----------------------------------------------------------------------------------------------------------------------- names(resAdj) ## ----------------------------------------------------------------------------- head(getAssociation(resAdj, "DiffMean")) head(getAssociation(resAdj, "DiffVar")) ## ----get Probe Res several coefs---------------------------------------------- head(getProbeResults(resAdj, rid = 1, coef = 2:3, fNames = c("chromosome", "start"))) ## ----getGeneVals-------------------------------------------------------------- getGeneVals(resAdj, "ARMS2", genecol = "UCSC_RefGene_Name", fNames = c("chromosome", "start")) ## ----Manhattan 1-------------------------------------------------------------- targetRange <- GRanges("23:13000000-23000000") plot(resAdj, rid = "DiffMean", type = "manhattan", highlight = targetRange) plot(resAdj, rid = "DiffMean", type = "manhattan", subset = targetRange) ## ----Manhattan 2-------------------------------------------------------------- plot(resAdj, rid = "DiffMean", type = "manhattan", suggestiveline = 3, genomewideline = 6, main = "My custom Manhattan") abline(h = 13, col = "yellow") ## ----Volcano 1---------------------------------------------------------------- plot(resAdj, rid = "DiffMean", type = "volcano", tPV = 14, tFC = 0.4, show.labels = FALSE) + ggtitle("My custom Volcano") ## ----QQ----------------------------------------------------------------------- plot(resAdj, rid = "DiffMean", type = "qq") + ggtitle("My custom QQplot") ## ----Plot_Features, warning = FALSE------------------------------------------- plotFeature(set = meth, feat = "cg09383816", variables = "status") + ggtitle("Diff Means") plotFeature(set = meth, feat = "cg11847929", variables = "status") + ggtitle("Diff Vars") ## ----Regional plot 1---------------------------------------------------------- targetRange <- GRanges("chrX:13000000-14000000") plotRegion(resAdj, targetRange) ## ----Regional plot 2---------------------------------------------------------- plotRegion(resAdj, targetRange, results = c("DiffMean"), tPV = 10) ## ----DiffMean, eval = FALSE--------------------------------------------------- # resDM <- runDiffMeanAnalysis(set = meth, model = ~ status) ## ----DiffVar, eval = FALSE---------------------------------------------------- # resDV <- runDiffVarAnalysis(set = meth, model = ~ status, coefficient = 2) ## ----RDA---------------------------------------------------------------------- targetRange <- GRanges("chrX:13000000-23000000") resRDA <- runRDA(set = meth, model = ~ status, range = targetRange) ## ----RDA res------------------------------------------------------------------ getAssociation(resRDA, rid = "RDA") ## ----getRDAresults------------------------------------------------------------ getRDAresults(resRDA) ## ----topRDAhits--------------------------------------------------------------- topRDAhits(resRDA) ## ----plotRDA------------------------------------------------------------------ plotRDA(object = resRDA, pheno = colData(meth)[, "status", drop = FALSE]) ## ----plotRDA 2---------------------------------------------------------------- plotRDA(object = resRDA, pheno = colData(meth)[, "status", drop = FALSE]) abline(h = -1) ## ----session Info------------------------------------------------------------- sessionInfo()