# #设置,包括= FALSE ----------------------------------------------------- knitr: opts_chunk设置(echo = TRUE) #美元预加载,以避免加载消息库(NanoMethViz) exon_tibble < - get_exons_mm10 () ## ---- eval = FALSE ------------------------------------------------------------ # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages(“BiocManager”)# # BiocManager::安装(“NanoMethViz ") ## ----------------------------------------------------------------------------- 库(NanoMethViz ) ## ----------------------------------------------------------------------------- # 甲基化甲基< -系统tabix文件中存储的数据。文件(包= " NanoMethViz”、“methy_subset.tsv.bgz”)# tabix只是一个特殊的gzip文件read.table标签分隔值(gzfile(甲基)col.names = methy_col_names (), nrows = 6 ) ## ----------------------------------------------------------------------------- # helper函数提取外显子从TxDb包exon_tibble < - get_exons_mm10()头(exon_tibble ) ## ----------------------------------------------------------------------------- 示例< - c(“B6Cast_Prom_1_bl6”,“B6Cast_Prom_1_cast”、“B6Cast_Prom_2_bl6”、“B6Cast_Prom_2_cast”、“B6Cast_Prom_3_bl6”、“B6Cast_Prom_3_cast”)组< - c(“bl6”、“铸造”,“bl6”,“演员”,“bl6”,“投”)sample_anno < - data.frame sample_anno(样本、组stringsAsFactors = FALSE) ## ----------------------------------------------------------------------------- nmeth_results < NanoMethResult(甲基、sample_anno exon_tibble ) ## ----------------------------------------------------------------------------- plot_gene (nmeth_results“Peg3 ") ## ----------------------------------------------------------------------------- # 加载保存结果从先前的bsseq分析bsseq_dmr < -阅读。表(系统。文件(包= " NanoMethViz”、“dmr_subset.tsv.gz”),9 =“t \”,标题= TRUE stringsAsFactors = FALSE ) ## ----------------------------------------------------------------------------- plot_gene (nmeth_results“Peg3 anno_regions = bsseq_dmr ) ## ---- 警告= FALSE --------------------------------------------------------- # 这个描述的警告已经关闭,但这通常会#产生许多警告的平滑读取会失败plot_gene (nmeth_results,“Peg3 anno_regions = bsseq_dmr,意大利面= TRUE ) ## ---- 警告= FALSE --------------------------------------------------------- plot_gene (nmeth_results“Peg3 anno_regions = bsseq_dmr热图= TRUE)