## ------------------------------------------------------------------------ library(CRISPRseek) library(BSgenome.Hsapiens.UCSC.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) outputDir <- file.path(getwd(),"CRISPRseekDemo") inputFilePath <- system.file('extdata', 'inputseq.fa', package = 'CRISPRseek') REpatternFile <- system.file('extdata', 'NEBenzymes.fa', package = 'CRISPRseek') ## ------------------------------------------------------------------------ ?offTargetAnalysis ?compare2Sequences ?CRISPRseek browseVignettes('CRISPRseek') ## ------------------------------------------------------------------------ offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, findPairedgRNAOnly = 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 = TRUE, BSgenomeName = Hsapiens, chromToSearch ="chrX", min.gap = 0, max.gap = 20, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, max.mismatch = 2, outputDir = outputDir, overwrite = TRUE) ## ------------------------------------------------------------------------ offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile, findPairedgRNAOnly = 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)