## ----setup, echo=FALSE--------------------------------------------------- knitr::opts_chunk$set(cache=TRUE) ## ------------------------------------------------------------------------ x <- rnorm(1000) # atomic vectors y <- x + rnorm(1000, sd=.5) df <- data.frame(x=x, y=y) # object of class 'data.frame' plot(y ~ x, df) # generic plot, method plot.formula fit <- lm(y ~x, df) # object of class 'lm' methods(class=class(fit)) # introspection ## ----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))