# #——风格,回声= FALSE,结果= '飞机 '-------------------------------------------------------- BiocStyle:减价()选项(宽度= 100,max.print = 1000) knitr:: opts_chunk设置(eval = as.logical (Sys美元。采用“KNITR_EVAL”,“真正的”)),缓存= as.logical (Sys。采用“KNITR_CACHE”,“真正的”)),警告= FALSE,消息= FALSE) # #——download_latest eval = FALSE ------------------------------------------------------------------ # systemPipeR_Intro.Rmd download.file (" https://raw.githubusercontent.com/tgirke/systemPipeRdata/master/vignettes/systemPipeR_Intro.Rmd "。 ") ## ---- 安装,eval = FALSE -------------------------------------------------------------------------- # 源(“//www.andersvercelli.com/biocLite.R”)# biocLite来源。安装脚本# biocLite("systemPipeR") #安装systemPipeR # biocLite("systemPipeRdata") #安装systemPipeRdata ## ----文档，eval = FALSE -------------------------------------------------------------------- # 库(systemPipeR) #加载包#库(帮助=“systemPipeR”)#包列表信息#装饰图案(systemPipeR) # # #打开一幕——genRna_workflow,eval = FALSE ------------------------------------------------------------------ # 库(systemPipeRdata) # genWorkenvir(工作流=“rnaseq”)# setwd(“rnaseq ") ## ---- targetsSE eval = TRUE ------------------------------------------------------------------------- 库(systemPipeR) targetspath < -系统。file("extdata"， "targets.txt"， package="systemPipeR")字符 = "#") ## ---- targetsPE eval = TRUE ------------------------------------------------------------------------- targetspath < -系统。file("extdata"， "targetsPE.txt"， package="systemPipeR")char = " # ")[1:2, 1:6) # #——comment_lines eval = TRUE --------------------------------------------------------------------- readline (targetspath)[1:4] # #——targetscomp eval = TRUE ----------------------------------------------------------------------- readComp(文件= targetspath格式=“向量”,delim ="-") ## ---- param_structure,eval = TRUE ------------------------------------------------------------------- parampath < -系统。文件(“extdata”、“大礼帽。param”,包= " systemPipeR ") ## ---- param_import eval = TRUE ---------------------------------------------------------------------- 参数< - suppressWarnings (systemArgs (sysma = parampath mytargets = targetspath)) args # #——sysarg_access eval = TRUE --------------------------------------------------------------------- 名(args) # #——sysarg_access2,eval = TRUE -------------------------------------------------------------------- sysargs (args)[1]模块(args)核(args) outpaths (args)[1] # #——sysarg_json eval = TRUE ----------------------------------------------------------------------- systemArgs (sysma = parampath mytargets = targetspath, type="json") ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()