# #——选项,结果=“隐藏”,回声= FALSE -------------------------------------- # 选项(宽度= 65)选项(useFancyQuotes = FALSE,继续= " ",位数= 3)# #——引用,eval = TRUE ---------------------------------------------------------- 引用(“QuasR ") ## ---- 安装,eval = FALSE ------------------------------------------------------ # 如果(!需要(“BiocManager”))# install.packages (BiocManager) # BiocManager::安装(“QuasR ") ## ---- loadLibraries,eval = TRUE ------------------------------------------------- suppressPackageStartupMessages({库(QuasR)图书馆(BSgenome)图书馆(Rsamtools)图书馆(rtracklayer)图书馆(GenomicFeatures)库(Gviz ) }) ## ---- help1 eval = FALSE -------------------------------------------------------- # help.start () ## ---- loadQuasRLibrary eval = FALSE --------------------------------------------- # 库(QuasR) # #——help2,eval = FALSE -------------------------------------------------------- # ? preprocessReads # #——help3 eval = FALSE -------------------------------------------------------- # 帮助(“preprocessReads ") ## ---- 分配,eval = FALSE ------------------------------------------------------- # x < - 2 # # - ls, eval = FALSE ----------------------------------------------------------- # ls () ## ---- printObject eval = FALSE -------------------------------------------------- # x SampleSession1 # #,eval = TRUE ------------------------------------------------ file.copy(系统。文件(包= " QuasR”、“extdata”),“。”,递归= TRUE) # #——SampleSession2 eval = TRUE ------------------------------------------------ sampleFile < - genomeFile < -“extdata / samples_chip_single.txt extdata / hg19sub。足总“项目< qAlign (sampleFile genomeFile)项目# #——SampleSession3 eval = TRUE ------------------------------------------------ extdata / qc_report.pdf qQCReport(项目。 ") ## ---- SampleSession4 eval = TRUE ------------------------------------------------ 库(rtracklayer)库(GenomicFeatures) annotFile < -“extdata / hg19sub_annotation。gtf" txStart <- import. txt "gff(注释文件，格式= "gtf"，功能。type =" start_codon") promReg <- promoters(txStart, upstream = 500, downstream = 500) names(promReg) <- mcols(promReg)$transcript_name promCounts <- qCount(proj, query = promReg) promCounts ## ----sampleFileSingle, echo=FALSE, results="asis"----------------------------- cat(paste(readLines(system。文件(包=“QuasR”、“extdata”、“samples_chip_single.txt”)),崩溃= " \ n ")) ## ---- sampleFilePaired,回声= FALSE,结果= "飞机 "----------------------------- 猫(粘贴(readline(系统。文件(包=“QuasR”、“extdata”、“samples_rna_paired.txt”)),崩溃= " \ n ")) ## ---- sampleFile eval = FALSE --------------------------------------------------- # sampleFile1 < -系统。# sampleFile2 <- system. file(package="QuasR"， "extdata"， # "samples_chip_single.txt")文件(包=“QuasR”、“extdata”#”samples_rna_paired.txt ") ## ----