# #——包括= FALSE --------------------------------------------------------- knitr: opts_chunk美元集(fig.width = 8,崩溃= TRUE,发表评论 = "#>" ) ## ---- 风格,回声= FALSE,结果= '飞机 '------------------------------------ BiocStyle:减价 () ## ---- 设置,消息= F -------------------------------------------------------- 图书馆(knitr) # #——信息在肉的论文认定,eval = FALSE ---------------------------------- # 数据(“CpGs_in_MEAT envir =环境 ()) ## ---- 信息在MEAT2.0论文认定,eval = FALSE ------------------------------- # 数据(“CpGs_in_MEAT2.0 envir =环境 ()) ## ---- 肉包安装,eval = FALSE ------------------------------------ # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“肉 ") ## ---- 肉包安装加载消息= FALSE,警告= FALSE ---------- 图书馆(肉)# #——甲基化矩阵表示 ------------------------------------------ 数据(“GSE121961 envir =环境 ()) ## ---- 甲基化矩阵表示表、回声= FALSE ---------------------- kable(头(GSE121961),## ----表型表表示--------------------------------------------- data("GSE121961_pheno"， environment = environment()) ## ----表型表表示表，echo =FALSE ------------------------- kable(GSE121961_pheno, caption = "GSE121961对应的表型。")## ----数据格式化，message=FALSE，警告= FALSE ---------------------------- 图书馆(SummarizedExperiment) GSE121961_SE < SummarizedExperiment(化验=(β= GSE121961)列表,colData = GSE121961_pheno) GSE121961_SE # #——数据清理,消息= FALSE,警告= FALSE ------------------------------ GSE121961_SE_clean < - clean_beta (SE = GSE121961_SE version = " MEAT2.0 ") ## ---- 数据清理桌子,回声= FALSE ---------------------------------------- kable(头(化验(GSE121961_SE_clean)β美元),标题= " GSE121961β清洗后矩阵的行 .") ## ---- 数据校准,消息= FALSE,警告= FALSE --------------------------- GSE121961_SE_calibrated < - BMIQcalibration (SE = GSE121961_SE_clean version = " MEAT2.0 ") ## ---- 数据校准表,回声= FALSE --------------------------------------- kable(头(化验(GSE121961_SE_calibrated)β美元),## ----校准前后的DNA甲基化分布，message=FALSE, warning=FALSE---- data("gold.mean. meat2.0 "， environment = environment()) GSE121961_SE_clean_with_gold_mean <- cbind(assays(GSE121961_SE_clean)$beta, gold.mean. meat2.0 $gold.mean) #添加黄金平均值GSE121961_SE_calibrated_with_gold_mean <- cbind(assays(gse121961_se_calibration)$beta，gold.mean. meat2.0 $gold.mean) #添加黄金均值组<- c(rep("GSE121961"， ncol(GSE121961_SE_clean))， "黄金均值")库(minfi) par(mfrow = c(2,1)) densityPlot(GSE121961_SE_clean_with_gold_mean, sampGroups = groups, main = "校正前"，legend =FALSE) densityPlot(GSE121961_SE_calibrated_with_gold_mean, sampGroups = groups, main = "校正后")## ----表观遗传年龄估计与表型，message=FALSE，警告= FALSE——GSE121961_SE_epiage < - epiage_estimation (SE = GSE121961_SE_calibrated age_col_name =“年龄”,version = " MEAT2.0 ") ## ---- 表观遗传的年龄估计与表型表,回声= FALSE -------------- kable (colData (GSE121961_SE_epiage),标题= "相应表型与AAdiff GSE121961为每个样本 .") ## ---- 会话信息 ------------------------------------------------------------- sessionInfo ()