# #——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 ------------------------------------------------------------------ 库(easyRNASeq) # #——vignetteData回声= FALSE ------------------------------------------------- vDir < - vignetteData () ## ---- P trichocarpa注释,eval = FALSE ------------------------------------- # download.file (url = paste0 (" ftp://ftp.plantgenie.org/Data/PopGenIE/ " # " Populus_trichocarpa / v3.0 / v10.1 GFF3 /”,#“Ptrichocarpa_210_v3.0_gene_exons.gff3.gz”),# destfile = " . / Ptrichocarpa_210_v3.0_gene_exons.gff3.gz ") ## ---- P trichocarpa注释下载,回声= FALSE ---------------------------- file.copy (dir (vDir模式=“* Ptrichocarpa_210_v3.0_gene_exons.gff3.gz full.names = TRUE),”。/ Ptrichocarpa_210_v3.0_gene_exons.gff3.gz ") ## ---- 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,eval = FALSE ---------------------------------------------------- # download.file (url = paste0 (" ftp://ftp.plantgenie.org/Tutorials/RnaSeqTutorial/ " #“数据/明星/ md5.txt”),# destfile = " md5.txt ") ## ---- 数据,eval = FALSE --------------------------------------------------------- # 数据(RobinsonDelhomme2014) #拉普兰人(RobinsonDelhomme2014[1:6,“文件名”],函数(f) {# # # download.file BAM文件(url = paste0 (" ftp://ftp.plantgenie.org/Tutorials/ " #“RnaSeqTutorial /数据/明星/ f),# destfile=as.character(f)) ## BAM索引文件# download.file(url=paste0("ftp://ftp.plantgenie.org/Tutorials/"， # "RnaSeqTutorial/data/star/"，f，".bai")， # destfile=as.character(paste0(f，".bai"))) #}) ## ----数据单元测试，eval=TRUE，echo=FALSE------------------------------------ #这是一个数据的子集(chr 19仅)用于加快#小装饰的创建，同时仍然测试能力数据(RobinsonDelhomme2014) lapply(RobinsonDelhomme2014[1:6，"Filename"]，函数(f){# BAM文件文件。copy(dir(vDir,pattern=paste0(as.character(f)，"$")，full.names=TRUE)，file.path("."，f)) # BAM索引文件文件。复制(dir (vDir、模式= paste0 (as.character (f),“.bai”),full.names = TRUE), file.path(“。”,paste0 (.bai f。 "))) }) ## ---- bamParam ----------------------------------------------------------------- bamParam < - bamParam (= TRUE,困= FALSE) # #——bamFiles ----------------------------------------------------------------- bamFiles < - getBamFileList (dir (".","*\\. bam美元”),dir (".","*\\. 白 $")) ## ---- rnaSeqParam -------------------------------------------------------------- rnaSeqParam < rnaSeqParam (annotParam = annotParam bamParam = bamParam countBy =“基因”,精度= "阅读 ") ## ---- 更简单的 ----------------------------------------------------------------- sexp1 < simpleRNASeq (bamFiles = bamFiles参数= rnaSeqParam verbose = TRUE) # #——清理,回声= FALSE ------------------------------------------------------ 数据(RobinsonDelhomme2014)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”,RobinsonDelhomme2014[1:6,“文件名”],paste0 (RobinsonDelhomme2014[1:6,“文件名”],”.bai "))) ## ---- 会话信息,回声= FALSE ------------------------------------------------- sessionInfo ()