## ----loadlib, echo=TRUE-------------------------------------------------- library(CRISPRseekGUIDEseqBioc2017Workshop) library(GUIDEseq) library(BSgenome.Hsapiens.UCSC.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) ## ---- helpFun, echo=TRUE, eval=FALSE------------------------------------- # help(GUIDEseqAnalysis) # help(combineOfftargets) # browseVignettes("GUIDEseq") ## ----SpCas9-1Lib, eval=TRUE---------------------------------------------- umi.inputfile <- c(system.file("extdata", "plusLibraryUMI.txt", package = "CRISPRseekGUIDEseqBioc2017Workshop"), system.file("extdata", "minusLibraryUMI.txt", package = "CRISPRseekGUIDEseqBioc2017Workshop")) alignment.inputfile <- c(system.file("extdata","plusLibrary.sort.bam" , package = "CRISPRseekGUIDEseqBioc2017Workshop"), system.file("extdata","minusLibrary.sort.bam" , package = "CRISPRseekGUIDEseqBioc2017Workshop")) gRNA.file <- system.file("extdata","gRNA.fa", package = "GUIDEseq") guideSeqRes <- GUIDEseqAnalysis( alignment.inputfile = alignment.inputfile, umi.inputfile = umi.inputfile, gRNA.file = gRNA.file, orderOfftargetsBy = "peak_score", descending = TRUE, BSgenomeName = Hsapiens, min.reads = 80, n.cores.max = 4) guideSeqRes$offTargets ## ----setLocalInputFile, eval=FALSE--------------------------------------- # library(GUIDEseq) # gRNA.file <- "~/GUIDEseqSpCas9Input/SpCas9gRNAexample.fa" # alignment.inputfile <- c("~/GUIDEseqSpCas9Input/plusLibrary.sort.bam", # "~/GUIDEseqSpCas9Input/minusLibrary.sort.bam") # umi.inputfile <- c("~/GUIDEseqSpCas9Input/plusLibraryUMI.txt", # "~/GUIDEseqSpCas9Input/minusLibraryUMI.txt") # outputDir <- "~/guideSeqResults" # guideSeqResults <- GUIDEseqAnalysis( # alignment.inputfile = alignment.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)