## ----dependencies, warning=FALSE, message=FALSE-------------------------- library(BSgenome) library(BSgenome.Scerevisiae.UCSC.sacCer2) ## ----biocLite, eval=FALSE------------------------------------------------ ## source("http://www.bioconductor.org/biocLite.R") ## biocLite(c("BSgenome", "BSgenome.Scerevisiae.UCSC.sacCer2")) ## ----BSgenome------------------------------------------------------------ available.genomes() library("BSgenome.Scerevisiae.UCSC.sacCer2") Scerevisiae ## ----BSgenomeLength------------------------------------------------------ seqlengths(Scerevisiae) seqnames(Scerevisiae) ## ----BSgenomeLoad-------------------------------------------------------- Scerevisiae$chrI ## ----gcChrI-------------------------------------------------------------- letterFrequency(Scerevisiae$chrI, "CG", as.prob = TRUE) ## ----gcGenome------------------------------------------------------------ param <- new("BSParams", X = Scerevisiae, FUN = letterFrequency) head(bsapply(param, letters = "GC")) ## ----gcGenome2----------------------------------------------------------- param <- new("BSParams", X = Scerevisiae, FUN = letterFrequency, simplify = TRUE) bsapply(param, letters = "GC") ## ----gcGenome3----------------------------------------------------------- sum(bsapply(param, letters = "GC")) / sum(seqlengths(Scerevisiae)) ## ----sessionInfo, echo=FALSE--------------------------------------------- sessionInfo()