# #——风格,回声= FALSE,结果= '飞机 '------------------------------------ BiocStyle::减价(css。= c(“custom.css文件 ')) ## ---- 回声= FALSE ------------------------------------------------------------ suppressPackageStartupMessages({库(rtracklayer)图书馆(GenomicRanges)图书馆(RNAmodR.RiboMethSeq)库(RNAmodR.Data ) }) ## ---- eval = FALSE ------------------------------------------------------------ # 库(rtracklayer) #库(GenomicRanges) #库(RNAmodR.RiboMethSeq) #库(RNAmodR.Data ) ## ---- 消息= FALSE,结果= '隐藏 '------------------------------------------- 注释< - GFF3File (RNAmodR.Data.example.RMS.gff3())序列< - RNAmodR.Data.example.RMS.fasta()文件< -列表(“Sample1”= c(治疗= RNAmodR.Data.example.RMS.1()),“Sample2”= c (= RNAmodR.Data.example.RMS.2治疗 ())) ## ----------------------------------------------------------------------------- msrms < ModSetRiboMethSeq(文件、注释=注释=序列)msrms序列 ## ----------------------------------------------------------------------------- 表< - read.csv2 (RNAmodR.Data.snoRNAdb (), stringsAsFactors = FALSE)表< -表(表hgnc_id美元= = " 53533 "]RNA5.8S # #子集只保留当前坐标表< -表[1 l: 7 l] snoRNAdb < -农庄(seqnames =“chr1”,范围= IRanges(美元开始=表位置、宽度= 1),链= " + " type =“RNAMOD mod =表修改美元,父母=“1”,#这是活动的记录id = IRanges:: CharacterList (strsplit(表美元指南”、“)))coord <分裂(snoRNAdb, snoRNAdb父母 ) ## ----------------------------------------------------------------------------- 范围(msrms)别名< data.frame (tx_id = " 1 " name = 5.8 s rRNA, stringsAsFactors = FALSE) # #——plot1 fig.cap =“热图显示RiboMethSeq分数来2 ' - o甲基化在5.8 s rRNA的立场。”---- plotCompareByCoord(msrms[c(2L,1L)]， coord, alias = alias) ## ---- plot2, fig.cap="RiboMethSeq scores around Um(14) on 5.8S rRNA."， fig.asp=1---- singleCoord <- coord[[1L]][1L，] plotDataByCoord(msrms, singleCoord) ## ---- plot3, fig.cap="RiboMethSeq scores around Um(14) on 5.8S rRNA."序列数据通过设置' showSequenceData = TRUE ' ."， fig.asp=1---- singleCoord <- coord[[1L]][1L，] plotDataByCoord(msrms, singleCoord, showSequenceData = TRUE) ## ----plot4, fig.cap="TPR vs FPR plot."，fig.asp = 1 ------------------------- plotROC (msrms coord) # #——设置 ----------------------------------------------------------------- 设置(msrms) < -列表(minScoreMean = 0.7) msrms # #——udpate ------------------------------------------------------------------- msrms2 < -修改(msrms力= TRUE ) ## ---- sessioninfo ------------------------------------------------------------- sessionInfo ()