## ----'installDer', eval = FALSE------------------------------------------
## ## try http:// if https:// URLs are not supported
## source("https://bioconductor.org/biocLite.R")
## biocLite("derfinderHelper")
## 
## ## Check that you have a valid Bioconductor installation
## biocValid()

## ----'citation'----------------------------------------------------------
## Citation info
citation('derfinderHelper')

## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE-----------
## Track time spent on making the vignette
startTime <- Sys.time()

## Bib setup
library('knitcitations')

## Load knitcitations with a clean bibliography
cleanbib()
cite_options(hyperlink = 'to.doc', citation_format = 'text', style = 'html')
# Note links won't show for now due to the following issue
# https://github.com/cboettig/knitcitations/issues/63

## Write bibliography information
bibs <- c(knitcitations = citation('knitcitations'),
    derfinderHelper = citation('derfinderHelper')[1], 
    #BiocStyle = citation('BiocStyle'),
    BiocStyle = RefManageR::BibEntry(bibtype = 'unpublished', key = 'BiocStyle', title = 'BiocStyle: Standard styles for vignettes and other Bioconductor documents', author = 'Martin Morgan and Andrzej Oleś and Wolfgang Huber', note = 'R package version 1.8.0', year = '2015'), 
    knitr = citation('knitr')[3],
    rmarkdown = citation('rmarkdown'),
    #BiocParallel = citation('BiocParallel'),
    BiocParallel = RefManageR::BibEntry(bibtype = 'unpublished', key = 'BiocParallel', title = 'BiocParallel: Bioconductor facilities for parallel evaluation', author = 'Martin Morgan and Valerie Obenchain and Michel Lang and Ryan Thompson', note = 'R package version 1.5.0', year = '2015'),
    R = citation(),
    IRanges = citation('IRanges'),
    Matrix = citation('Matrix'),
    #S4Vectors = citation('S4Vectors'),
    S4Vectors = RefManageR::BibEntry(bibtype = 'unpublished', key = 'S4Vectors', title = 'S4Vectors: S4 implementation of vectors and lists', author = 'H. Pages and M. Lawrence and P. Aboyoun', note = 'R package version 0.9.6', year = '2015'),
    devtools = citation('devtools'),
    testthat = citation('testthat'))
write.bibtex(bibs,
    file = 'derfinderHelperRef.bib')
bib <- read.bibtex('derfinderHelperRef.bib')

## Assign short names
names(bib) <- names(bibs)

## ----'createData'--------------------------------------------------------
## Create some toy data
suppressPackageStartupMessages(library('IRanges'))
set.seed(20140923)
toyData <- DataFrame(
    'sample1' = Rle(sample(0:10, 1000, TRUE)),
    'sample2' = Rle(sample(0:10, 1000, TRUE)),
    'sample3' = Rle(sample(0:10, 1000, TRUE)),
    'sample4' = Rle(sample(0:10, 1000, TRUE)),
    'sample5' = Rle(sample(0:15, 1000, TRUE)),
    'sample6' = Rle(sample(0:15, 1000, TRUE)),
    'sample7' = Rle(sample(0:15, 1000, TRUE)),
    'sample8' = Rle(sample(0:15, 1000, TRUE)),
    'sample9' = Rle(sample(0:20, 1000, TRUE)),
    'sample10' = Rle(sample(0:20, 1000, TRUE)),
    'sample11' = Rle(sample(0:20, 1000, TRUE)),
    'sample12' = Rle(sample(0:20, 1000, TRUE)),
    'sample13' = Rle(sample(0:100, 1000, TRUE)),
    'sample14' = Rle(sample(0:100, 1000, TRUE)),
    'sample15' = Rle(sample(0:100, 1000, TRUE)),
    'sample16' = Rle(sample(0:100, 1000, TRUE))
)

## Lets say that we have 4 groups
group <- factor(rep(toupper(letters[1:4]), each = 4))

## Note that some groups have higher coverage, we can adjust for this in the model
sampleDepth <- sapply(toyData, sum)
sampleDepth

## ----'createModels'------------------------------------------------------
## Build the model matrices
mod <- model.matrix(~ sampleDepth + group)
mod0 <- model.matrix(~ sampleDepth)

## Explore them
mod
mod0

## ----'calculateFstats'---------------------------------------------------
library('derfinderHelper')
fstats <- fstats.apply(data = toyData, mod = mod, mod0 = mod0, scalefac = 1)
fstats

## ----createVignette, eval=FALSE------------------------------------------
## ## Create the vignette
## library('rmarkdown')
## system.time(render('derfinderHelper.Rmd', 'BiocStyle::html_document'))
## 
## ## Extract the R code
## library('knitr')
## knit('derfinderHelper.Rmd', tangle = TRUE)

## ----createVignette2-----------------------------------------------------
## Clean up
file.remove('derfinderHelperRef.bib')

## ----reproducibility1, echo=FALSE----------------------------------------
## Date the vignette was generated
Sys.time()

## ----reproducibility2, echo=FALSE----------------------------------------
## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits=3)

## ----reproducibility3, echo=FALSE----------------------------------------
## Session info
library('devtools')
options(width = 120)
session_info()

## ----vignetteBiblio, results = 'asis', echo = FALSE, warning = FALSE-----
## Print bibliography
bibliography()