# #——loadlib回声= TRUE -------------------------------------------------- 库(CRISPRseekGUIDEseqBioc2017Workshop)库(GUIDEseq)图书馆(BSgenome.Hsapiens.UCSC.hg19)图书馆(TxDb.Hsapiens.UCSC.hg19.knownGene)库(org.Hs.eg.db ) ## ---- helpFun,呼应= TRUE, eval = FALSE ------------------------------------- # 帮助(GUIDEseqAnalysis) # # browseVignettes(“GUIDEseq (combineOfftargets) ") ## ---- SpCas9-1Lib eval = TRUE ---------------------------------------------- umi。inputfile < - c(系统。文件(“extdata”，“pluslibraryum .txt”，包=“CRISPRseekGUIDEseqBioc2017Workshop”)，系统。文件(“extdata”，“minuslibraryum .txt”，包=“CRISPRseekGUIDEseqBioc2017Workshop”))对齐。inputfile < - c(执行(“extdata”、“plusLibrary.sort。系统文件(“extdata”，“minusLibrary.sort”，“minusLibrary.sort”)。bam"， package = "CRISPRseekGUIDEseqBioc2017Workshop")) gRNA。文件< -执行(“extdata”、“gRNA。guideSeqRes <- GUIDEseqAnalysis(对齐). fa"， package = "GUIDEseq")inputfile =对齐。inputfile umi。inputfile = umi。inputfile gRNA。文件= gRNA。guideSeqRes$offTargets ## ----setLocalInputFile, eval=FALSE--------------------------------------- # library(GUIDEseq) # gRNA. conf . conf . conf . conf . conf . conf . conf . conf . conf . conf . conf . conf . conf . conf . conf文件~ / GUIDEseqSpCas9Input / SpCas9gRNAexample < -”。足总“#对齐。inputfile < - c(“~ / GUIDEseqSpCas9Input / plusLibrary.sort。# "~/GUIDEseqSpCas9Input/minusLibrary.sort.bam")inputfile <- c("~/GUIDEseqSpCas9Input/plusLibraryUMI.txt"， # "~/GUIDEseqSpCas9Input/minusLibraryUMI.txt") # outputDir <- "~/guideSeqResults" # guideSeqResults <- GUIDEseqAnalysis(# alignment. txt);inputfile =对齐。inputfile # umi。inputfile = umi。inputfile, # gRNA.file = gRNA.file, # BSgenomeName = Hsapiens, # outputDir = outputDir) ## ----annotateOff, eval=TRUE---------------------------------------------- library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) outputDir <- "~/guideSeqResults" guideSeqResults <- GUIDEseqAnalysis( alignment.inputfile = alignment.inputfile, umi.inputfile = umi.inputfile, gRNA.file = gRNA.file, BSgenomeName = Hsapiens, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, outputDir = outputDir) ## ----mergeOff, echo=FALSE------------------------------------------------ offtarget.folder <- system.file("extdata", c("sample2-18", "sample3-19", "sample4-20"), package = "GUIDEseq") mergedOfftargets <- combineOfftargets(offtarget.folder = offtarget.folder, sample.name = c("Wild-type SpCas9", "SpCas9-MT3-ZFP", "Split-SpCas9 dual NLS"), outputFileName = "TS2offtargets3Constructs.xls") head(mergedOfftargets)