I dont understand the following instructions in crisprseek attachment 8. I tried to follow when hit rock bottom.
outputDir <- getwd()
does that mean i type in (i)outputDir or (ii)getwd() or (iii)outputDir <- getwd() ? (i) when i type in outputdir, it givees me  "C:/Users/Jit Ming/Documents/doc 1
does that mean i have set the output directory?
inputFilePath <- "X.fa"
does that mean I type in "inputFilePath"?
REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek")
I dont understand how REpatternFile is done too? can someone please help me with REpatternFIle and offtargetAnalysis? I do not knwo hwo you bring up inputfilepath, findgRNAswithREcutonly command ........
offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE,
REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, max.mismatch = 3, chromToSearch = "", outputDir = outputDir, overwrite = TRUE)
Sorry I am big time computer-illiterate.