## ----style, echo = FALSE, results = 'asis'-------------------------------------------------------- BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))) ## ----packages, eval=TRUE, echo=FALSE, warning=FALSE, message=FALSE-------------------------------- suppressPackageStartupMessages({ library(BioC2016Introduction) library(SummarizedExperiment) library(airway) }) ## ----configure-test------------------------------------------------------------------------------- stopifnot( getRversion() >= '3.3' && getRversion() < '3.4', BiocInstaller::biocVersion() == "3.4" ) ## ------------------------------------------------------------------------------------------------- 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 ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()