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Create vignette (#62)
* Update DESCRIPTION * Create MMAPPR2.rmd * Update MMAPPR2.rmd * Update MMAPPR2.rmd * Update MMAPPR2.rmd * Update MMAPPR2.rmd * Update README.md * Update README.md * Update MMAPPR2.rmd * Update README.md * Update MMAPPR2.rmd * Update minMapQuality doc * Remove ref genome * remove need for chr5_distance object * Remove need for dummy_distance object * Remove need for dummy_distance object * Refactor chr5 MD objects to data folder * Add data files * Update MMAPPR2.rmd * Rename read_bam to distance * Try dynamic examples on mmappr * Document data * Try to fix tests * Update and rename MMAPPR2.rmd to MMAPPR2.Rmd * Update MMAPPR2.Rmd * Update MmapprParam show method * BAM files in extdata * Refactor to use extdata BAMs * Update MMAPPR2.Rmd * Add MMAPPR2data to mmappr and calculateDistance docs * Use intermediate MDs in docs * Install MMAPPR2data in Travis script * Use only dummy BAM in tests * Fix file validity * Update tests for new data * Index every file in BamFileList * Remove skipDebug * Update README.md * Redo MD objects * Update tests for new data * Remove old test BAM files, update README * Update MMAPPR2.Rmd * Update docs to match MMAPPR2data change * Remove .addBamFileIndex from validity check * Delete extdata * Bump version * Update docs * Fix doc error * Change system() to system2() * Update MMAPPR2.Rmd * Change back to system; system2 was failing * Remove index warning when building param * Try lazyload=yes * Travis: only devel * Update MMAPPR2.Rmd * Update DESCRIPTION * Update DESCRIPTION * Update MMAPPR2.Rmd * Try installing ExperimentHub from GitHub * Update vignette * Remove debug sys.which * Try using bioc-devel * Try bioc-devel again * Update vignette * Try bioc-devel again * sudo: false on travis * Update vignette * Try another travis build, without sudo * Update vignette * Remove username from sample objects * Try possibleDates() again * Update vignette * Try GitHub BiocManager and sudo=required * Try ask=false * Add fake GmapGenomeDirectory to get examples to run * Update docs with examples * Add fake VEP for param example * Bump version to 0.98.11 * Create directories for examples * Create directories for examples * Create gmap and DEFAULT directories in vignette * Update MMAPPR2.Rmd * Fix Biocpkg * See if outputMmapprData caused weird cleanEx dev.off problem * Reinstate outputMmapprData example, comment out prePeak example, which was causing weird failure * Update docs * Try comment out prePeak example again (fixed) * Uncomment prePeak, didn't make a difference * Don't run both outputMmapprData examples in both places * Update docs * Fix merge * Sudo required in .travis.yml * Don't run VEPFlags block * Track down cannot allocate memory problem * Track down error * More tracking down error * Try only running steps, only use postCandidatesMD * Try without MD objects * Explicitly load MMAPPR2data data * Fix @candidates problem in vignette * Remove RDS file reading--cannot open connection bug * Update post_loess_dummy_md to fix param * Remove MD objects from tests * Make examples not runnable * Missed one * Remove data from package * Update docs
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‎DESCRIPTION‎

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Package: MMAPPR2
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Title: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
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Version: 0.98.10
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Version: 0.98.11
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Authors@R: c(
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person("Kyle", "Johnsen", email="kjohnsen@byu.edu", role=c("aut")),
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person('Nathaniel', 'Jenkins', role=c('aut')),
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LazyData: true
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LazyLoad: yes
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RoxygenNote: 6.1.0
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VignetteBuilder: knitr
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Suggests: testthat,
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mockery,
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roxygen2,
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knitr,
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rmarkdown,
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BiocStyle,
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MMAPPR2data
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Imports: ensemblVEP (>= 1.20.0),
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gmapR,

‎R/aicc_loess.R‎

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#' of the \code{distance} slot list filled.
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#'
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#' @examples
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#' \dontrun{
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#' postLoessMD <- loessFit(postCalcDistMD)
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#' }
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#' @export
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loessFit <- function(mmapprData) {
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loessOptResolution <- mmapprData@param@loessOptResolution

‎R/data.R‎

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‎R/main.R‎

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#' # Run pipeline:
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#' mmapprData <- mmappr(mmapprParam)
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#'
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#' ### Alternately, you can navigate the pipeline step by step.
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#' ### This may be helpful for debugging.
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#' md <- new('MmapprData', param = mmapprParam)
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#' postCalcDistMD <- calculateDistance(md)
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#' postLoessMD <- loessFit(postCalcDistMD)
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#' postPrePeakMD <- prePeak(postLoessMD)
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#' postPeakRefMD <- peakRefinement(postPrePeakMD)
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#' \dontrun{postCandidatesMD <- generateCandidates(postPeakRefMD)
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#' outputMmapprData(postCandidatesMD)
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#' }
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#' }
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#' \dontrun{
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#' ### Alternately, you can navigate the pipeline step by step.
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#' ### This may be helpful for debugging.
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#' md <- new('MmapprData', param = mmapprParam)
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#' postCalcDistMD <- calculateDistance(md)
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#' postLoessMD <- loessFit(postCalcDistMD)
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#' postPrePeakMD <- prePeak(postLoessMD)
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#' postPeakRefMD <- peakRefinement(postPrePeakMD)
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#' postCandidatesMD <- generateCandidates(postPeakRefMD)
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#' outputMmapprData(postCandidatesMD)
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#' }
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#'
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#' @seealso \code{\link{calculateDistance}}, \code{\link{loessFit}},
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#' \code{\link{prePeak}}, \code{\link{peakRefinement}},

‎R/output.R‎

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#' @export
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#'
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#' @examples
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#' dir.create(outputFolder(param(postCandidatesMD))) ## Ignore this line
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#' \dontrun{outputMmapprData(postCandidatesMD)}
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#' \dontrun{
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#' outputMmapprData(postCandidatesMD)
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#' }
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outputMmapprData <- function(mmapprData) {
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stopifnot(class(mmapprData) == "MmapprData")
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oF <- outputFolder(param(mmapprData))

‎R/peaks.R‎

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#' @export
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#'
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#' @examples
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#' \dontrun{
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#' postPeakRefMD <- peakRefinement(postPrePeakMD)
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#' }
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peakRefinement <- function(mmapprData){
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mmapprData@peaks <-
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.runFunctionInParallel(mmapprData@peaks,
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#' @export
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#'
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#' @examples
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#' \dontrun{
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#' postPrePeakMD <- prePeak(postLoessMD)
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#' }
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prePeak <- function(mmapprData) {
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mmapprData@peaks <- list()
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‎README.md‎

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## Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
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### Kyle Johnsen, Nathaniel Jenkins, Jonathon Hill
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### [See vignette for instructions](vignettes/MMAPPR2.Rmd)
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MMAPPR2 maps mutations resulting from pooled RNA-seq data from the F2
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cross of forward genetic screens. Its predecessor is described in a paper published
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in Genome Research (Hill et al. 2013). MMAPPR2 accepts aligned BAM files as well as

‎data/postCalcDistMD.rda‎

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‎data/postCandidatesMD.rda‎

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‎data/postLoessMD.rda‎

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