表观遗传分析-DNA甲基化芯片-数据预处理

##DNA methylation ##首先下载Target OS甲基化数据及临床数据 ##https://portal.gdc.cancer.gov/projects/TARGET-OS 这个界面下载的临床数据 260709 ##同时看到甲基化数据有86例，258个数据文件 ##BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19") library(IlluminaHumanMethylation450kanno.ilmn12.hg19) library(minfi) library(illuminaio) library(readr) library(data.table) library(dplyr) anno - getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19) anno - as.data.frame(anno) anno$probe - rownames(anno) p4ha1_anno - anno[grepl("(^|;)P4HA1(;|$)", anno$UCSC_RefGene_Name), ] ##从整个 450K 芯片注释表 anno 里面，筛选出所有被注释到 P4HA1 基因的 CpG 探针，并保存为 p4ha1_anno p4ha1_anno[, c( "probe", "chr", "pos", "UCSC_RefGene_Name", "UCSC_RefGene_Group", "Relation_to_Island" )] ##查看检索到的甲基化位点 P4HA1_ALL_CpG_beta_matrix - read_csv("DNA methylation/P4HA1_ALL_CpG_beta_matrix.csv") View(P4HA1_ALL_CpG_beta_matrix) dim(P4HA1_ALL_CpG_beta_matrix) p4ha1_beta_t - as.data.frame(t(P4HA1_ALL_CpG_beta_matrix[, -1])) c