inst/doc/regionReport.R

In regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

## ----'installDer', eval = FALSE---------------------------------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE)) {
#        install.packages("BiocManager")
#    }
#  
#  BiocManager::install("regionReport")
#  
#  ## Check that you have a valid Bioconductor installation
#  BiocManager::valid()

## ----'citation'-------------------------------------------------------------------------------------------------------
## Citation info
citation("regionReport")

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

## Bib setup
library("RefManageR")

## Write bibliography information
bib <- c(
    derfinder = citation("derfinder")[1],
    regionReport = citation("regionReport")[1],
    knitrBootstrap = citation("knitrBootstrap"),
    BiocStyle = citation("BiocStyle"),
    ggbio = citation("ggbio"),
    ggplot2 = citation("ggplot2"),
    knitr = citation("knitr")[3],
    RefManageR = citation("RefManageR")[1],
    rmarkdown = citation("rmarkdown")[1],
    DT = citation("DT"),
    R = citation(),
    IRanges = citation("IRanges"),
    sessioninfo = citation("sessioninfo"),
    GenomeInfoDb = RefManageR::BibEntry(
        bibtype = "manual",
        key = "GenomeInfoDb",
        author = "Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès",
        title = "GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers",
        year = 2017, doi = "10.18129/B9.bioc.GenomeInfoDb"
    ),
    GenomicRanges = citation("GenomicRanges"),
    biovizBase = citation("biovizBase"),
    TxDb.Hsapiens.UCSC.hg19.knownGene = citation("TxDb.Hsapiens.UCSC.hg19.knownGene"),
    derfinderPlot = citation("derfinderPlot")[1],
    grid = citation("grid"),
    gridExtra = citation("gridExtra"),
    mgcv = citation("mgcv"),
    RColorBrewer = citation("RColorBrewer"),
    whikser = citation("whisker"),
    bumphunter = citation("bumphunter")[1],
    pheatmap = citation("pheatmap"),
    DESeq2 = citation("DESeq2"),
    edgeR1 = citation("edgeR")[1],
    edgeR2 = citation("edgeR")[2],
    edgeR6 = RefManageR::BibEntry("inbook",
        key = "edgeR6",
        author = "Chen, Yunshun and Lun, Aaron T. L. and Smyth, Gordon K.",
        title = "Differential expression analysis of complex RNA-seq experiments using edgeR",
        booktitle = "Statistical Analysis of Next Generation Sequencing Data",
        year = 2014,
        editor = "Datta, Somnath and Nettleton, Dan", publisher = "Springer",
        location = "New York", pages = "51-74"
    ),
    DEFormats = citation("DEFormats")
)

## ----overviewNotRun, eval = FALSE-------------------------------------------------------------------------------------
#  ## Load derfinder
#  library("derfinder")
#  regions <- genomeRegions$regions
#  
#  ## Assign chr length
#  library("GenomicRanges")
#  seqlengths(regions) <- c("chr21" = 48129895)
#  
#  ## The output will be saved in the 'derfinderReport-example' directory
#  dir.create("renderReport-example", showWarnings = FALSE, recursive = TRUE)
#  
#  ## Generate the HTML report
#  report <- renderReport(regions, "Example run",
#      pvalueVars = c(
#          "Q-values" = "qvalues", "P-values" = "pvalues"
#      ), densityVars = c(
#          "Area" = "area", "Mean coverage" = "meanCoverage"
#      ),
#      significantVar = regions$qvalues <= 0.05, nBestRegions = 20,
#      outdir = "renderReport-example"
#  )

## ----loadDerfinder----------------------------------------------------------------------------------------------------
## Load derfinder
library("derfinder")

## The output will be saved in the "derfinderReport-example" directory
dir.create("derfinderReport-example", showWarnings = FALSE, recursive = TRUE)

## ----runDerfinderFake, eval=FALSE-------------------------------------------------------------------------------------
#  ## Save the current path
#  initialPath <- getwd()
#  setwd(file.path(initialPath, "derfinderReport-example"))
#  
#  ## Generate output from derfinder
#  
#  ## Collapse the coverage information
#  collapsedFull <- collapseFullCoverage(list(genomeData$coverage),
#      verbose = TRUE
#  )
#  
#  ## Calculate library size adjustments
#  sampleDepths <- sampleDepth(collapsedFull,
#      probs = c(0.5), nonzero = TRUE,
#      verbose = TRUE
#  )
#  
#  ## Build the models
#  group <- genomeInfo$pop
#  adjustvars <- data.frame(genomeInfo$gender)
#  models <- makeModels(sampleDepths, testvars = group, adjustvars = adjustvars)
#  
#  ## Analyze chromosome 21
#  analysis <- analyzeChr(
#      chr = "21", coverageInfo = genomeData, models = models,
#      cutoffFstat = 1, cutoffType = "manual", seeds = 20140330, groupInfo = group,
#      mc.cores = 1, writeOutput = TRUE, returnOutput = TRUE
#  )
#  
#  ## Save the stats options for later
#  optionsStats <- analysis$optionsStats
#  
#  ## Change the directory back to the original one
#  setwd(initialPath)

## ----runDerfinderReal-------------------------------------------------------------------------------------------------
## Copy previous results
file.copy(system.file(file.path("extdata", "chr21"),
    package = "derfinder",
    mustWork = TRUE
), "derfinderReport-example", recursive = TRUE)

## ----mergeResults-----------------------------------------------------------------------------------------------------
## Merge the results from the different chromosomes. In this case, there's
## only one: chr21
mergeResults(
    chrs = "chr21", prefix = "derfinderReport-example",
    genomicState = genomicState$fullGenome
)

## Load optionsStats
load(file.path("derfinderReport-example", "chr21", "optionsStats.Rdata"), verbose = TRUE)

## ----loadLib, message=FALSE-------------------------------------------------------------------------------------------
## Load derfindeReport
library("regionReport")

## ----createReport, eval = FALSE---------------------------------------------------------------------------------------
#  ## Generate the HTML report
#  report <- derfinderReport(
#      prefix = "derfinderReport-example", browse = FALSE,
#      nBestRegions = 15, makeBestClusters = TRUE,
#      fullCov = list("21" = genomeDataRaw$coverage), optionsStats = optionsStats
#  )

## ----vignetteBrowse, eval=FALSE---------------------------------------------------------------------------------------
#  ## Browse the report
#  browseURL(report)

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

## ----createVignette2--------------------------------------------------------------------------------------------------
## Clean up
unlink("derfinderReport-example", recursive = TRUE)

## ----vignetteReproducibility1, echo=FALSE-----------------------------------------------------------------------------
## Date the report was generated
Sys.time()

## ----vignetteReproducibility2, echo=FALSE-----------------------------------------------------------------------------
## Processing time in seconds
totalTimeVignette <- diff(c(startTimeVignette, Sys.time()))
round(totalTimeVignette, digits = 3)

## ----vignetteReproducibility3, echo=FALSE-----------------------------------------------------------------------------
## Session info
library("sessioninfo")
options(width = 120)
session_info()

## ----vignetteBiblio, results='asis', echo=FALSE, warning = FALSE, message = FALSE-------------------------------------
## Print bibliography
PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))