### R code from vignette source 'CRISPRseek.Rnw' ################################################### ### 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:285-288 ################################################### 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:295-304 ################################################### results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, annotateExon = FALSE,findPairedgRNAOnly = TRUE, chromToSearch = "chrX", max.mismatch = 0, BSgenomeName = Hsapiens, rule.set = "CRISPRscan", baseBeforegRNA = 6, baseAfterPAM = 6, featureWeightMatrixFile = system.file("extdata", "Morenos-Mateo.csv", package = "CRISPRseek"), outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 11: CRISPRseek.Rnw:315-322 ################################################### 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 12: CRISPRseek.Rnw:343-348 ################################################### 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 13: CRISPRseek.Rnw:360-367 ################################################### results <- offTargetAnalysis(inputFilePath, annotatePaired = FALSE, scoring.method = "CFDscore", PAM.pattern = "NNG$|NGN$", chromToSearch = "chrX", annotateExon = FALSE, max.mismatch = 2, BSgenomeName = Hsapiens, outputDir = outputDir, overwrite = TRUE) ################################################### ### code chunk number 14: CRISPRseek.Rnw:379-389 ################################################### offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, findPairedgRNAOnly = FALSE, annotatePaired = FALSE, BSgenomeName = Hsapiens, chromToSearch = "chrX", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 4, outputDir = outputDir, overwrite = TRUE, PAM.location = "5prime", PAM = "TGT", PAM.pattern = "^T[A|G]N", allowed.mismatch.PAM = 2, subPAM.position = c(1,2), baseEditing = TRUE, editingWindow = 10:20, targetBase = "A") ################################################### ### code chunk number 15: CRISPRseek.Rnw:419-437 ################################################### resultsIndelF <- offTargetAnalysis( inputFilePath, findgRNAsWithREcutOnly = FALSE, findPairedgRNAOnly = FALSE, annotatePaired = FALSE, BSgenomeName = Hsapiens, chromToSearch = "chrX", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, outputDir = outputDir, overwrite = TRUE, scoring.method = "CFDscore", PAM.pattern = "NNG$|NGN$", predIndelFreq = TRUE) if(exists("resultsIndelF")) { print(head(resultsIndelF$indelFreq[[1]])) mapply(write.table, resultsIndelF$indelFreq, file=paste0(names(resultsIndelF$indelFreq), '.xls'), sep = "\t", row.names = FALSE) } ################################################### ### code chunk number 16: CRISPRseek.Rnw:485-486 ################################################### sessionInfo()