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
jonathonthill · Oct 18, 2018 · c529d38 · c529d38
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MMAPPR2
 Title: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
-Version: 0.98.10
+Version: 0.98.11
 Authors@R: c(
     person("Kyle", "Johnsen", email="kjohnsen@byu.edu", role=c("aut")),
     person('Nathaniel', 'Jenkins', role=c('aut')),
@@ -17,9 +17,13 @@ Encoding: UTF-8
 LazyData: true
 LazyLoad: yes
 RoxygenNote: 6.1.0
+VignetteBuilder: knitr
 Suggests: testthat,
     mockery,
     roxygen2,
+    knitr,
+    rmarkdown,
+    BiocStyle,
     MMAPPR2data
 Imports: ensemblVEP (>= 1.20.0),
     gmapR,

diff --git a/R/aicc_loess.R b/R/aicc_loess.R
@@ -9,7 +9,9 @@
 #'   of the \code{distance} slot list filled.
 #'   
 #' @examples 
+#' \dontrun{
 #' postLoessMD <- loessFit(postCalcDistMD)
+#' }
 #' @export
 loessFit <- function(mmapprData) {
     loessOptResolution <- mmapprData@param@loessOptResolution

diff --git a/R/data.R b/R/data.R
diff --git a/R/main.R b/R/main.R
@@ -38,17 +38,18 @@
 #'     # Run pipeline:
 #'     mmapprData <- mmappr(mmapprParam)
 #' 
-#'     ### Alternately, you can navigate the pipeline step by step.
-#'     ### This may be helpful for debugging.
-#'     md <- new('MmapprData', param = mmapprParam)
-#'     postCalcDistMD <- calculateDistance(md)
-#'     postLoessMD <- loessFit(postCalcDistMD)
-#'     postPrePeakMD <- prePeak(postLoessMD)
-#'     postPeakRefMD <- peakRefinement(postPrePeakMD)
-#'     \dontrun{postCandidatesMD <- generateCandidates(postPeakRefMD)
-#'     outputMmapprData(postCandidatesMD)
-#'     }
 #' }
+#' \dontrun{
+#' ### Alternately, you can navigate the pipeline step by step.
+#' ### This may be helpful for debugging.
+#' md <- new('MmapprData', param = mmapprParam)
+#' postCalcDistMD <- calculateDistance(md)
+#' postLoessMD <- loessFit(postCalcDistMD)
+#' postPrePeakMD <- prePeak(postLoessMD)
+#' postPeakRefMD <- peakRefinement(postPrePeakMD)
+#' postCandidatesMD <- generateCandidates(postPeakRefMD)
+#' outputMmapprData(postCandidatesMD)
+#' } 
 #' 
 #' @seealso \code{\link{calculateDistance}}, \code{\link{loessFit}},
 #'   \code{\link{prePeak}}, \code{\link{peakRefinement}},

diff --git a/R/output.R b/R/output.R
@@ -8,8 +8,9 @@
 #' @export
 #'
 #' @examples
-#' dir.create(outputFolder(param(postCandidatesMD))) ## Ignore this line
-#' \dontrun{outputMmapprData(postCandidatesMD)}
+#' \dontrun{
+#' outputMmapprData(postCandidatesMD)
+#' }
 outputMmapprData <- function(mmapprData) {
     stopifnot(class(mmapprData) == "MmapprData")
     oF <- outputFolder(param(mmapprData))

diff --git a/R/peaks.R b/R/peaks.R
@@ -10,7 +10,9 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' postPeakRefMD <- peakRefinement(postPrePeakMD)
+#' }
 peakRefinement <- function(mmapprData){
     mmapprData@peaks <- 
         .runFunctionInParallel(mmapprData@peaks,
@@ -100,7 +102,9 @@ peakRefinement <- function(mmapprData){
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' postPrePeakMD <- prePeak(postLoessMD)
+#' }
 prePeak <- function(mmapprData) {
     mmapprData@peaks <- list()
 

diff --git a/README.md b/README.md
@@ -4,6 +4,8 @@
 ## Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
 ### Kyle Johnsen, Nathaniel Jenkins, Jonathon Hill
 
+### [See vignette for instructions](vignettes/MMAPPR2.Rmd)
+
 MMAPPR2 maps mutations resulting from pooled RNA-seq data from the F2
 cross of forward genetic screens. Its predecessor is described in a paper published
 in Genome Research (Hill et al. 2013). MMAPPR2 accepts aligned BAM files as well as

diff --git a/data/postCalcDistMD.rda b/data/postCalcDistMD.rda
diff --git a/data/postCandidatesMD.rda b/data/postCandidatesMD.rda
diff --git a/data/postLoessMD.rda b/data/postLoessMD.rda
diff --git a/data/postPeakRefMD.rda b/data/postPeakRefMD.rda
diff --git a/data/postPrePeakMD.rda b/data/postPrePeakMD.rda
diff --git a/man/loessFit.Rd b/man/loessFit.Rd
diff --git a/man/mmappr.Rd b/man/mmappr.Rd
diff --git a/man/outputMmapprData.Rd b/man/outputMmapprData.Rd
diff --git a/man/peakRefinement.Rd b/man/peakRefinement.Rd
diff --git a/man/postCalcDistMD.Rd b/man/postCalcDistMD.Rd
diff --git a/man/postCandidatesMD.Rd b/man/postCandidatesMD.Rd
diff --git a/man/postLoessMD.Rd b/man/postLoessMD.Rd
diff --git a/man/postPeakRefMD.Rd b/man/postPeakRefMD.Rd
diff --git a/man/postPrePeakMD.Rd b/man/postPrePeakMD.Rd
diff --git a/man/prePeak.Rd b/man/prePeak.Rd
diff --git a/tests/testthat/test_candidates.R b/tests/testthat/test_candidates.R
@@ -1,14 +1,14 @@
 context("Variant calling and effect prediction")
 
-mmapprData <- postPeakRefMD
+mmapprData <- readRDS('test_data/objects/post_peakref_dummy_md.RDS')
 
 
 test_that("ranges for peaks are prepared", {
-    candList <- .getPeakRange(mmapprData@peaks$chr5)
+    peakList <- list(seqname='7', start=44309092, end=67669545)
+    candList <- .getPeakRange(peakList)
     expect_s4_class(candList, 'GRanges')
-    chr5PeakList <- mmapprData@peaks$chr5
     expect_equal(BiocGenerics::width(candList),
-                 chr5PeakList$end - chr5PeakList$start + 1)
+                 peakList$end - peakList$start + 1)
 })
 
 
@@ -37,7 +37,7 @@ test_that('.getVariantsForRange returns VRanges with sample names', {
     expect_s4_class(result, 'VRanges')
     expect_equal(as.character(GenomicRanges::seqnames(result))[1], 'chr5')
     expect_equal(as.character(Biobase::sampleNames(result))[1],
-                 'zy13mut.bam')
+                 'zy14_dummy.bam')
 })
 
 

diff --git a/tests/testthat/test_data/objects/post_loess_dummy_md.RDS b/tests/testthat/test_data/objects/post_loess_dummy_md.RDS
diff --git a/tests/testthat/test_loess.R b/tests/testthat/test_loess.R
@@ -49,9 +49,12 @@ test_that(".localResolution works right", {
 
 })
 
-test_that("peak chromosome is fit correctly", {
-    mdChr7 <- postCalcDistMD
-    chr7list <- mdChr7@distance$`7`
+test_that("chromosome is fit correctly", {
+    set.seed(1)
+    chr7list <- list(distanceDf=data.frame(
+        pos=seq_len(1000),
+        distance=stats::rnorm(1000, 0.01, sd = 0.0005)
+    ), wtCounts=1, mutCounts=1)
     chr7list <- expect_warning(.loessFitForChr(
         chr7list,
         loessOptResolution = .001,
@@ -62,8 +65,8 @@ test_that("peak chromosome is fit correctly", {
         c("wtCounts", "mutCounts", "loess", "aicc") %in%
             names(chr7list)
     ))
-    expect_gt(length(chr7list$loess$x), 4000)
-    expect_equal(chr7list$loess$pars$span, 0.069)
+    expect_equal(length(chr7list$loess$x), 1000)
+    expect_equal(chr7list$loess$pars$span, 0.919)
 })
 
 

diff --git a/tests/testthat/test_output.R b/tests/testthat/test_output.R
@@ -1,6 +1,7 @@
 context('Output functions')
 
-mmapprData <- postCandidatesMD
+mmapprData <- readRDS('test_data/objects/post_peakref_dummy_md.RDS')
+
 
 test_that('default output folder is prepared correctly', {
     skip_if_not_installed('mockery')