## ----style, echo = FALSE, results = 'asis'--------------------------------------------------------
BiocStyle::markdown()
options(width=100, max.print=1000)

## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE--------------------------------------------
knitr::opts_chunk$set(cache=TRUE)
suppressPackageStartupMessages({
    library(Biostrings)
    library(GenomicRanges)
})

## ----setup-objects--------------------------------------------------------------------------------
library(Biostrings)
library(GenomicRanges)

## ----Biostrings, message=FALSE--------------------------------------------------------------------
library(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]

## ----methods, eval=FALSE--------------------------------------------------------------------------
#  methods(class=class(phiX174Phage))      # 'DNAStringSet' methods

## ----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))

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

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