## ----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()