## ----dependencies, warning=FALSE, message=FALSE-------------------------- library(Biostrings) library(BSgenome) library(BSgenome.Scerevisiae.UCSC.sacCer2) ## ----biocLite, eval=FALSE------------------------------------------------ ## source("http://www.bioconductor.org/biocLite.R") ## biocLite(c("Biostrings", "BSgenome", ## "BSgenome.Scerevisiae.UCSC.sacCer2", "AnnotationHub")) ## ----mmatchPattern------------------------------------------------------- dnaseq <- DNAString("ACGTACGT") matchPattern(dnaseq, Scerevisiae$chrI) countPattern(dnaseq, Scerevisiae$chrI) vmatchPattern(dnaseq, Scerevisiae) head(vcountPattern(dnaseq, Scerevisiae)) ## ----revCompCheck-------------------------------------------------------- dnaseq == reverseComplement(dnaseq) ## ----sessionInfo, echo=FALSE--------------------------------------------- sessionInfo()