### R code from vignette source 'CRISPRseek.Rnw' ### Encoding: UTF-8 ################################################### ### code chunk number 1: style ################################################### BiocStyle::latex() ################################################### ### code chunk number 2: CRISPRseek.Rnw:131-138 ################################################### library(CRISPRseek) library(BSgenome.Hsapiens.UCSC.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) outputDir <- getwd() inputFilePath <- system.file('extdata', 'inputseq.fa', package = 'CRISPRseek') REpatternFile <- system.file('extdata', 'NEBenzymes.fa', package = 'CRISPRseek') ################################################### ### code chunk number 3: CRISPRseek.Rnw:166-172 ################################################### results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile, findPairedgRNAOnly = TRUE, BSgenomeName = Hsapiens, chromToSearch ="chrX", min.gap = 0, max.gap = 20, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 0,overlap.gRNA.positions = c(17, 18), outputDir = outputDir,overwrite = TRUE) ################################################### ### code chunk number 4: CRISPRseek.Rnw:185-191 ################################################### results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile,findPairedgRNAOnly = TRUE, BSgenomeName = Hsapiens, chromToSearch = "chrX", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 5: CRISPRseek.Rnw:203-209 ################################################### results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens, chromToSearch = "chrX", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 6: CRISPRseek.Rnw:222-228 ################################################### results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile,findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens, chromToSearch = "chrX", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 7: CRISPRseek.Rnw:240-249 ################################################### gRNAFilePath <- system.file('extdata', 'testHsap_GATA1_ex2_gRNA1.fa', package = 'CRISPRseek') results <- offTargetAnalysis(inputFilePath = gRNAFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, findgRNAs = FALSE, BSgenomeName = Hsapiens, chromToSearch = 'chrX', txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 8: CRISPRseek.Rnw:262-265 ################################################### results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, REpatternFile = REpatternFile,findPairedgRNAOnly = TRUE, chromToSearch = "", outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 9: CRISPRseek.Rnw:282-285 ################################################### results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, annotateExon = FALSE,findPairedgRNAOnly = TRUE, chromToSearch = "chrX", max.mismatch = 0, BSgenomeName = Hsapiens, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 10: CRISPRseek.Rnw:296-303 ################################################### inputFile1Path <- system.file("extdata", "rs362331C.fa", package = "CRISPRseek") inputFile2Path <- system.file("extdata", "rs362331T.fa", package = "CRISPRseek") REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek") seqs <- compare2Sequences(inputFile1Path, inputFile2Path, outputDir = outputDir , REpatternFile = REpatternFile, overwrite = TRUE) seqs ################################################### ### code chunk number 11: CRISPRseek.Rnw:324-329 ################################################### results <- offTargetAnalysis(inputFilePath, annotatePaired = FALSE, chromToSearch = "chrX", enable.multicore = TRUE, n.cores.max = 10, annotateExon = FALSE, max.mismatch = 0, BSgenomeName = Hsapiens, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 12: CRISPRseek.Rnw:340-346 ################################################### results <- offTargetAnalysis(inputFilePath, annotatePaired = FALSE, scoring.method = "CFDscore", chromToSearch = "chrX", annotateExon = FALSE, max.mismatch = 2, BSgenomeName = Hsapiens, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 13: CRISPRseek.Rnw:374-375 ################################################### sessionInfo()