# #——风格,回声= FALSE,结果= '飞机 '----------------------------------- BiocStyle:减价 () ## ---- = = FALSE消息= FALSE,警告,结果“隐藏”,回声= FALSE --------------- 选项(数字= 2)# #——图书馆 ------------------------------------------------------------- 图书馆(easyRNASeq) # #——P trichocarpa注释 -------------------------------------------- 库(curl) curl_download (url = paste0(“ftp://ftp.plantgenie.org/Data/PopGenIE/”,“Populus_trichocarpa / v3.0 / v10.1 / GFF3 /”,Ptrichocarpa_210_v3.0_gene_exons.gff3.gz)。/ Ptrichocarpa_210_v3.0_gene_exons.gff3.gz destfile =。 ") ## ---- AnnotParam ---------------------------------------------------------- annotParam < - annotParam(数据源= " / Ptrichocarpa_210_v3.0_gene_exons.gff3.gz ") ## ---- 创建合成记录 ---------------------------------------- annotParam < - createSyntheticTranscripts (annotParam verbose = FALSE) # #——保存对象 ----------------------------------------------------- 保存(annotParam,文件/ Ptrichocarpa_210_v3.0_gene_exons_synthetic-transcripts_annotParam.rda = " ") ## ---- 创建合成记录作为胃肠道 ---------------------------------- gI < - createSyntheticTranscripts(“。/ Ptrichocarpa_210_v3.0_gene_exons.gff3.gz”verbose = FALSE) # #——导出文件 ----------------------------------------------------- writeGff3 (gI,文件/ Ptrichocarpa_210_v3.0_gene_exons_synthetic-transcripts.gff3.gz = " ") ## ---- bam文件 ----------------------------------------------------------- 库(curl) curl_download (url = paste0(“ftp://ftp.plantgenie.org/Tutorials/RnaSeqTutorial/”,“数据/明星/ md5.txt”),destfile = " md5.txt ") ## ---- 数据 ---------------------------------------------------------------- 数据(RobinsonDelhomme2014)拉普兰人(RobinsonDelhomme2014[1:6,“文件名”),函数(f) {curl_download (url = paste0(“ftp://ftp.plantgenie.org/Tutorials/”,“RnaSeqTutorial /数据/明星/ f), destfile = f ) }) ## ---- bamParam ------------------------------------------------------------ bamParam < - bamParam (= TRUE配对,困= FALSE) # #——rnaSeqParam --------------------------------------------------------- rnaSeqParam < rnaSeqParam (annotParam = annotParam bamParam = bamParam countBy =“基因”,精度= "阅读 ") ## ---- 会话信息,回声= FALSE -------------------------------------------- sessionInfo () ## ---- 清理,回声= FALSE ------------------------------------------------- 文件。remove(c("./Ptrichocarpa_210_v3.0_gene_exons.gff3.gz"， "./ ptrichocarpa_210_v3 .0_gene_exons_synthetic- transcripts_annotam .gz"， "./ ptrichocarpa_210_v3 .0_gene_exons_synthetic- transcripts_注解参数。rda”、“。/ Ptrichocarpa_210_v3.0_gene_exons_synthetic-transcripts.gff3.gz”))