## ----样式，echo = false，结果='asis'--------------------------------------------------------------------------- BiocStyle :: Markdown（CSS.Files = C（'Custom.css'））## ------------------------------------------------------------------------------------------------------------------------------------------ suppressPackageStartupMessages({ library(rtracklayer) library(GenomicRanges）库（rnamodr.ribomethseq）库（rnamodr.data）}）## ------------------------------------------------------------------------------------------------------------------------------------------＃library（rtracklayer）＃library（genomicranges）＃library（rnamodr.ribobomethseq）＃library（rnamodr.data）## ----消息= false，结果='hide'-------------------------------------------------------------------------------------------------------------------------------- annotation <- GFF3File(RNAmodR.Data.example.RMS.gff3()) sequences <- RNAmodR.Data.example.RMS.fasta() files <-列表（“ sample1” = c（处理= rnamodr.data.example.rms.1（）），“ sample2” = c（处理= rnamodr.data.example.rms.rms.2（）））## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- msrms <- ModSetRiboMethSeq(files, annotation = annotation, sequences = sequences) msrmS ## ---------------------------------------------------------------------------------------------------------------------------表<-table [表$ hgnc_id ==“ 53533”，]＃子集到RNA5.8S＃仅保留当前的坐标表<-table [，1l：7l：7l：7l：7l] snornadb <-granges（seqnames =“ chr1”，ranges = iranges = iranges = iranges = iranges（start = table $ position，width = 1），strand =“+”，type =“ rnamod”，mod = table $修改，parent =“ 1”，＃this是成绩单ID活动= iranges :: targinlist（strsplit（strsplit）（表$指南，“，”）））坐标< - split（Snornadb，snornadb $ parent）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ranges(msrms) alias <- data.frame(tx_id = "1", name = "5.8S rRNA", stringsAsFactors = FALSE) ## ----plot1, fig.cap="Heatmap showing RiboMethSeq scores for 2'-O methylated positions on the 5.8S rRNA."---- 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. Sequence data is shown by setting `showSequenceData = TRUE`.", fig.asp=1---- singleCoord <- coord[[1L]][1L,] plotDataByCoord(msrms, singleCoord, showSequenceData = TRUE) ## ----plot4, fig.cap="TPR versus FPR plot.", fig.asp=1------------------------- plotROC(msrms,coord) ## ----settings----------------------------------------------------------------- settings(msrms) <- list(minScoreMean = 0.7) msrms ## ----udpate------------------------------------------------------------------- msrms2 <- modify(msrms,force = TRUE) ## ---- sessioninfo------------------------------------------------------------- sessionInfo()