## ----style, echo = FALSE, results = 'asis'---------------------------------
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))

## ----setup, echo=FALSE-----------------------------------------------------
suppressPackageStartupMessages({
    library(Biostrings)
    library(GenomicRanges)
    library(SummarizedExperiment)
    library(airway)
    library(rtracklayer)
    library(ShortRead)
    library(GenomicAlignments)
    library(RNAseqData.HNRNPC.bam.chr14)
    library(VariantAnnotation)
})

## ----install, eval=FALSE---------------------------------------------------
#  source("https://bioconductor.org/biocLite.R")
#  biocLite(c("DESeq2", "org.Hs.eg.db"))

## ----require---------------------------------------------------------------
library(GenomicRanges)

## ----help-bioc, eval=FALSE-------------------------------------------------
#  help(package="GenomicRanges")
#  vignette(package="GenomicRanges")
#  vignette(package="GenomicRanges", "GenomicRangesHOWTOs")
#  ?GRanges

## ----five-lines------------------------------------------------------------
x <- rnorm(1000)
y <- x + rnorm(1000)
df <- data.frame(X=x, Y=y)
plot(Y ~ X, df)
fit <- lm(Y ~ X, df)
anova(fit)
abline(fit)

## ----help-r, eval=FALSE----------------------------------------------------
#  class(fit)
#  methods(class=class(fit))
#  methods(plot)
#  ?"plot"
#  ?"plot.formula"

## ----classes-and-methods---------------------------------------------------
library(Biostrings)
dna <- DNAStringSet(c("AACAT", "GGCGCCT"))
reverseComplement(dna)

## --------------------------------------------------------------------------
data(phiX174Phage)
phiX174Phage
letterFrequency(phiX174Phage, "GC", as.prob=TRUE)

## ----classes-and-methods-discovery, eval=FALSE-----------------------------
#  class(dna)
#  ?"DNAStringSet-class"
#  ?"reverseComplement,DNAStringSet-method"