Version 2.0 major update

ZarnackGroup · Jun 22, 2023 · 80de317 · 80de317
1 parent 49d9240
commit 80de317
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Showing 61 changed files with 5,300 additions and 1,199 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,25 +2,46 @@
 
 export(BSFDataSet)
 export(BSFDataSetFromBigWig)
+export(BSFind)
 export(annotateWithScore)
+export(assignToGenes)
+export(assignToTranscriptRegions)
 export(bindingSiteCoveragePlot)
 export(collapseReplicates)
 export(coverageOverRanges)
+export(duplicatedSitesPlot)
+export(estimateBsWidth)
+export(estimateBsWidthPlot)
+export(exportToBED)
+export(geneOverlapsPlot)
 export(getMeta)
 export(getRanges)
 export(getSignal)
 export(getSummary)
+export(globalScorePlot)
 export(makeBindingSites)
+export(makeBsSummaryPlot)
+export(mergeCrosslinkDiagnosticsPlot)
 export(mergeSummaryPlot)
+export(processingStepsFlowChart)
+export(processingStepsTable)
+export(pureClipGeneWiseFilter)
+export(pureClipGlobalFilter)
+export(pureClipGlobalFilterPlot)
 export(rangeCoveragePlot)
 export(reproducibilityFilter)
+export(reproducibilityFilterPlot)
+export(reproducibilitySamplesPlot)
 export(reproducibiliyCutoffPlot)
 export(setMeta)
 export(setRanges)
 export(setSignal)
 export(setSummary)
 export(supportRatio)
 export(supportRatioPlot)
+export(targetGeneSpectrumPlot)
+export(transcriptRegionOverlapsPlot)
+export(transcriptRegionSpectrumPlot)
 exportMethods("[")
 exportMethods(getMeta)
 exportMethods(getRanges)
@@ -31,20 +52,61 @@ exportMethods(setRanges)
 exportMethods(setSignal)
 exportMethods(setSummary)
 exportMethods(show)
+import(ComplexHeatmap)
 import(GenomicRanges)
-import(Gviz)
 import(ggplot2)
+import(lifecycle)
 import(methods)
+import(rtracklayer)
 import(tidyr)
 importFrom(GenomeInfoDb,keepSeqlevels)
 importFrom(GenomeInfoDb,seqlevels)
+importFrom(GenomicFeatures,cds)
+importFrom(GenomicFeatures,fiveUTRsByTranscript)
+importFrom(GenomicFeatures,genes)
+importFrom(GenomicFeatures,intronsByTranscript)
+importFrom(GenomicFeatures,threeUTRsByTranscript)
 importFrom(GenomicRanges,findOverlaps)
+importFrom(IRanges,extractList)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,count)
+importFrom(dplyr,desc)
+importFrom(dplyr,everything)
+importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
+importFrom(dplyr,lead)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,mutate_all)
+importFrom(dplyr,n)
+importFrom(dplyr,pull)
+importFrom(dplyr,reframe)
+importFrom(dplyr,rename)
+importFrom(dplyr,rename_with)
+importFrom(dplyr,row_number)
+importFrom(dplyr,select)
+importFrom(dplyr,slice)
+importFrom(dplyr,slice_head)
+importFrom(dplyr,slice_tail)
+importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
+importFrom(dplyr,ungroup)
 importFrom(ggforce,geom_mark_rect)
+importFrom(grDevices,colorRampPalette)
+importFrom(grid,gpar)
+importFrom(kableExtra,kable)
 importFrom(matrixStats,colSds)
 importFrom(plyr,rbind.fill)
 importFrom(rtracklayer,import)
+importFrom(stats,density)
 importFrom(stats,median)
 importFrom(stats,quantile)
+importFrom(stats,sd)
+importFrom(tibble,add_row)
+importFrom(tibble,rownames_to_column)
 importFrom(tidyr,pivot_longer)
+importFrom(utils,head)
+importFrom(utils,tail)
diff --git a/R/AllClasses.R b/R/AllClasses.R
@@ -8,7 +8,8 @@ BSFDataSet <- setClass(
         signal = "list",
         summary = "data.frame",
         params = "list",
-        plotData = "list"
+        plotData = "list",
+        results = "data.frame"
     )
 )
 setValidity("BSFDataSet", function(object) {
@@ -196,6 +197,7 @@ BSFDataSet <- function(ranges, meta, signal, dropSeqlevels = TRUE, silent = FALS
     summary = data.frame()
     params = list()
     plotData = list()
+    results = data.frame()
 
     # construct final object
     obj = new(
@@ -205,7 +207,8 @@ BSFDataSet <- function(ranges, meta, signal, dropSeqlevels = TRUE, silent = FALS
         signal = signal,
         summary = summary,
         params = params,
-        plotData = plotData
+        plotData = plotData,
+        results = results
     )
     return(obj)
 }

diff --git a/R/CoverageFunctions.R b/R/CoverageFunctions.R
@@ -114,7 +114,7 @@ coverageOverRanges <- function(
         )
     }
     if (returnOptions == "merge_positions_keep_replicates") {
-        covRet = .coverageOverRanges.merge_positions_keep_replicates( # TODO works for uneven ranges
+        covRet = .coverageOverRanges.merge_positions_keep_replicates(
             sgn = sgn, rng = rng, method = method
         )
     }
@@ -125,10 +125,6 @@ coverageOverRanges <- function(
     }
     return(covRet)
 }
-# TODO
-# output ranges are not sorted properly
-# -> remove silent option -> warnings should always be shown
-
 
 .coverageOverRanges.merge_positions_keep_replicates <- function(sgn, rng, method) {
 
@@ -186,9 +182,7 @@ coverageOverRanges <- function(
     }
     # sort ranges
     rngCov = c(retCov)
-    rngCov = GenomeInfoDb::sortSeqlevels(rngCov)
     rngCov = .sortRanges(rngCov)
-    # rngCov = sort(rngCov)
 
     return(rngCov)
 }