# #——风格,回声= FALSE,结果= '飞机 '------------------------------------ BiocStyle::减价(css。= c(“custom.css文件 ')) ## ---- 回声= FALSE -------------------------------------------------------------- suppressPackageStartupMessages({库(tRNAscanImport ) }) ## ----------------------------------------------------------------------------- 库(tRNAscanImport) yeast_file < -系统。File ("extdata"， File = "酵母。tRNAscan”,包= " tRNAscanImport”)为sacCer3 # #输出之前readline (con = yeast_file, n = 7 l ) ## ----------------------------------------------------------------------------- # 输出sacCer3 #后gr < - import.tRNAscanAsGRanges (yeast_file)头(gr, 2) #任何农庄组织传递,可用于后续函数istRNAscanGRanges (gr吗 ) ## ---- 回声= FALSE -------------------------------------------------------------- suppressPackageStartupMessages({库(Biostrings)库(rtracklayer ) }) ## ----------------------------------------------------------------------------- 库(Biostrings)库(rtracklayer) # suppressMessages(库(rtracklayer,静静地= TRUE)) #保存writeXStringSet tRNA序列(gr tRNA_seq美元,filepath = tempfile()) #是GFF3兼容使用tRNAscan2GFF gff <- tRNAscan2GFF(gr)导出。gff3(人造石铺地面,反对= tempfile ()) ## ----------------------------------------------------------------------------- # tRNAscan-SE输出hg38 human_file < -系统。File ("extdata"， File = "human. "tRNAscan"， package = "tRNAscanImport") # tRNAscan- se output for e.c oli MG1655 eco_file <- system. txt . txt . txt . txt . txt。File ("extdata"， File = "ecoli. "tRNAscan"， package = "tRNAscanImport") # import tRNAscan- se files gr_human <- import. trnascanasgranges (human_file) gr_eco <- import. trnascanasgranges (eco_file) # get summary plots grl <- GRangesList(Sce = gr, Hsa = gr_human, Eco = gr_eco) plots <- gettRNAFeaturePlots(grl) ## ----plot1, fig.cap = "tRNA长度。"------------------------------------------ 块长度# #美元——plot2 fig.cap = " tRNAscan-SE分数。"----------------------------------- 情节tRNAscan_score # #美元——plot3 fig.cap = " tRNA GC含量。"-------------------------------------- 情节gc # #美元——plot4 fig.cap = " trna与内含子。"----------------------------------- 情节tRNAscan_intron # #美元——plot5 fig.cap = "循环变量的长度。"-------------------------- 情节variableLoop_length # #美元——回声= FALSE -------------------------------------------------------------- suppressPackageStartupMessages({库(BSgenome.Scerevisiae.UCSC.sacCer3 ) }) ## ---- tRNA_precursor ----------------------------------------------------------- 库(BSgenome.Scerevisiae.UCSC.sacCer3)基因组< - getSeq (BSgenome.Scerevisiae.UCSC.sacCer3)染色体匹配tRNAscan #重命名输出名称(基因组)< - c(名字(基因组)(-17 l),“chrmt”)tRNAprecursor <- get.tRNAprecursor(gr, genome) head(tRNAprecursor) ## ----------------------------------------------------------------------------- sessionInfo()