## ----setup, echo=FALSE--------------------------------------------------- knitr::opts_chunk$set(cache=TRUE) ## ----Biostrings, message=FALSE------------------------------------------- require(Biostrings) # Biological sequences data(phiX174Phage) # sample data, see ?phiX174Phage phiX174Phage m <- consensusMatrix(phiX174Phage)[1:4,] # nucl. x position counts polymorphic <- which(colSums(m != 0) > 1) m[, polymorphic] ## ----showMethods, eval=FALSE--------------------------------------------- # showMethods(class=class(phiX174Phage), where=search()) ## ----phiX---------------------------------------------------------------- library(Biostrings) data(phiX174Phage) ## ----consensusMatrix----------------------------------------------------- m <- consensusMatrix(phiX174Phage)[1:4,] polymorphic <- which(colSums(m != 0) > 1) mapply(substr, polymorphic, polymorphic, MoreArgs=list(x=phiX174Phage)) ## ----iranges------------------------------------------------------------- library(IRanges) ir <- IRanges(start=c(10, 20, 30), width=5) ir ## ----iranges-flank------------------------------------------------------- flank(ir, 3) ## ----iranges-class------------------------------------------------------- class(ir) getClassDef(class(ir)) ## ----iranges-flank-method, eval=FALSE------------------------------------ # ?"flank,Ranges-method" ## ----granges------------------------------------------------------------- library(GenomicRanges) gr <- GRanges(c("chr1", "chr1", "chr2"), ir, strand=c("+", "-", "+")) gr ## ----granges-flank------------------------------------------------------- flank(gr, 3) ## ----granges-class------------------------------------------------------- class(gr) getClassDef(class(gr)) ## ----granges-flank-method, eval=FALSE------------------------------------ # ?"flank,GenomicRanges-method" ## ----granges-methods, eval=FALSE----------------------------------------- # showMethods(class="GRanges", where=search()) ## ----granges-man-and-vignettes, eval=FALSE------------------------------- # help(package="GenomicRanges") # vignette(package="GenomicRanges") # vignette(package="GenomicRanges", "GenomicRangesHOWTOs") ## ----require------------------------------------------------------------- library(GenomicRanges) ## ----help, eval=FALSE---------------------------------------------------- # help(package="GenomicRanges") # vignette(package="GenomicRanges") # vignette(package="GenomicRanges", "GenomicRangesHOWTOs") # ?GRanges