## --------------------------------------------------------------------------------------------图书馆（Crisprepeek）图书馆（Bsgenome.hsapiens.ucsc.hg19）库（Txdb.hsapiens.ucsc.hg19.knowngene）outputdir < - file.path（getwd（），“crispseekdemo”）inputfilepath < - system.file（'extdata'，'inputseq.fa'，package ='crispseek'）repatternfile < - system.file（'extdata'，'Nebenzymes.fa'，包='crispseek'）## ----------------------------------------------------------------？Offtargetanalysis？compare2序列？CrispreSeek Browsevignettes（'Crispseeek'）## ----------------------------------------------------------------------------------------- opptargetAnalysis（inpopFilePath，findgrnaswithrecutonly = false，repatternfile = repatternfile，findpairedgrnaonly = true，bsgenomename = hsapiens，chromtosearch =“chrx”，min.gap= 0，max.gap = 20，txdb = txdb.hsapiens.ucsc.hg19.kcokngene，max.mismatch = 0，outputdir = outputdir，覆盖= true）## ---------------------------------------------------------------------------------------落地tanalysis（InputGrnaSwithrecutonly = false，Repatternfile = Repatternfile，findPairedGraonly = True，Bsgenomename = Hsapiens，ChromTOSearch =“Chrx”，Min.gap = 0，Max.gap = 20，TXDB = TXDB.hsapiens.Cuc.hg19.knowngene，max.mismatch = 2，outputdir = outputdir，覆盖=真）## ------------------------------------------------------------------------------------ Offtargetanalysis（inputfilepath，findgrnaswithrecutonly = true，repatternfile = repatternfile，findpairedgrnally = true，bsgenomename = hsapiens，chromtosearch =“chrx”，min.gap = 0，max.gap = 20，txdb = txdb.hsapiens.ucsc.hg19.knowngene，max.mismatch = 0，outputdir = outputdir，overwrite = TRUE) ## ------------------------------------------------------------------------ offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens, chromToSearch ="chrX", min.gap = 0, max.gap = 20, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, max.mismatch = 3, outputDir = outputDir, overwrite = TRUE) ## ------------------------------------------------------------------------ offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens, chromToSearch ="chrX", min.gap = 0, max.gap = 20, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, max.mismatch = 0, outputDir = outputDir, overwrite = TRUE) ## ------------------------------------------------------------------------ gRNAFilePath <- system.file('extdata', 'testHsap_GATA1_ex2_gRNA1.fa', package = 'CRISPRseek') offTargetAnalysis(inputFilePath = gRNAFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, findgRNAs = FALSE, BSgenomeName = Hsapiens, chromToSearch = 'chrX', txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, max.mismatch = 2, outputDir = outputDir, overwrite = TRUE) ## ------------------------------------------------------------------------ offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile,findPairedgRNAOnly = TRUE, chromToSearch = "", outputDir = outputDir, overwrite = TRUE) ## ------------------------------------------------------------------------ inputFile1Path <- system.file("extdata", "rs362331C.fa", package = "CRISPRseek") inputFile2Path <- system.file("extdata", "rs362331T.fa", package = "CRISPRseek") seqs <- compare2Sequences(inputFile1Path, inputFile2Path, outputDir = outputDir , REpatternFile = REpatternFile, overwrite = TRUE)