## ----样式，echo = false，结果='asis'--------------------------------------------------------------------------- BiocStyle :: Markdown（CSS.Files = C（'Custom.css'））## ------------------------------------------------------------------------------------------------------------------------------------------ suppressPackageStartupMessages({ library(rtracklayer) library(GenomicRanges）库（rnamodr.alkanilineseq）库（rnamodr.data）}）## ------------------------------------------------------------------------------------------------------------------------------＃library（rtracklayer）＃library（genomicranges）＃library（rnamodr.alkanilineseq）＃library（rnamodr.data）## ----消息= false，结果='hide'-------------------------------------------------------------------------------------------------------------------------------- annotation <- GFF3File(RNAmodR.Data.example.AAS.gff3()) sequences <- RNAmodR.Data.example.AAS.fasta() files <-list（“ wt” = c（处理= rnamodr.data.example.wt.1（），处理= rnamodr.data.example.wt.2（），处理= rnamodr.data.example.wt.3（）），“ bud23del” = c（处理= rnamodr.data.example.bud23.1（），处理= rnamodr.data.example.bud23.2（）），“ trm8del” = c（处理= rnamodr.data.example。trm8.1（），处理= rnamodr.data.example.trm8.2（））## ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------msaas <-modsetalkanilineseq（文件，注释=注释，序列=序列）msaas ## ----------------------------------------------------------------------------------------------------------------------------------------------- mod <-修改（msaas）lapply（mod，head，n = 2l）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mod [[1L]] alias <- data.frame(tx_id = c(1L,3L,5L,6L,7L,8L,10L,11L), name = c("18S rRNA","tF(GAA)B","tG(GCC)B","tT(AGT)B", "tQ(TTG)B","tC(GCA)B","tS(CGA)C","tV(AAC)E1"), stringsAsFactors = FALSE) ## ----plot1, fig.cap="Heatmap showing Stop ratio scores for detected m7G, m3C and D positions.", fig.asp=1---- plotCompareByCoord(msaas, coord, score = "scoreSR", alias = alias, normalize = TRUE) ## ----plot2, fig.cap="Heatmap showing Stop ratio scores for detected m7G1575 on the 18S rRNA.", fig.asp=0.5---- plotCompareByCoord(msaas, coord[1L], score = "scoreSR", alias = alias) ## ----plot3, fig.cap="Stop ratio scores for detected m7G1575 on the 18S rRNA plotted as bar plots along the sequence.", fig.asp=1---- plotData(msaas, "1", from = 1550L, to = 1600L) ## ----plot4, fig.cap="Stop ratio scores for detected m7G1575 on the 18S rRNA plotted as bar plots along the sequence. The raw sequence data is shown by setting `showSequenceData = TRUE.", fig.asp=1---- plotData(msaas[1L:2L], "1", from = 1550L, to = 1600L, showSequenceData = TRUE) ## ---- sessioninfo------------------------------------------------------------- sessionInfo()