include a new function to evaluate overlaps

Author: Lucille Delisle

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: analysePeaks
 Title: Compare, annotate your peaks
-Version: 0.1.1
+Version: 1.0.0
 Authors@R: 
     person(given = "Lucille",
            family = "Lopez-Delisle",
@@ -11,7 +11,7 @@ Description: This package will compare peaks (usually narrow peaks). It can be c
 License: CC BY 4.0
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.0
 Imports:
     grDevices,
     graphics,
@@ -21,7 +21,8 @@ Imports:
     GenomicRanges,
     stats,
     pheatmap,
-    reshape
+    reshape,
+    igraph
 Suggests: 
     testthat (>= 2.1.0),
     knitr,

NAMESPACE

@@ -4,14 +4,14 @@ export(annotateWithCate)
 export(barplotFromNamedVector)
 export(cateNamesFromThreshold)
 export(createMyGRs)
+export(createMyGRsUsingSimpleOverlap)
 export(plotAllBarPlotForCategoriesFromMyGR)
 export(plotAllPheatmapsFor2CategoriesFromMyGR)
 export(plotCateComparisonSetAndRef)
 export(plotClassicalHistogramForMyGRs)
 export(plotPairwiseComparison)
 export(writeNarrowPeaksFromMyGRsAndAnnot)
 export(writeTablesFromMyGRsAndAnnot)
-import(stats)
 importFrom(GenomicRanges,distanceToNearest)
 importFrom(GenomicRanges,end)
 importFrom(GenomicRanges,findOverlaps)
@@ -25,7 +25,19 @@ importFrom(graphics,hist)
 importFrom(graphics,legend)
 importFrom(graphics,par)
 importFrom(graphics,plot)
+importFrom(igraph,add_vertices)
+importFrom(igraph,components)
+importFrom(igraph,graph_from_edgelist)
+importFrom(igraph,vcount)
 importFrom(pheatmap,pheatmap)
 importFrom(reshape,cast)
+importFrom(stats,aggregate)
+importFrom(stats,cor.test)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,quantile)
+importFrom(usefulLDfunctions,subsetByNamesOrIndices)
+importFrom(usefulLDfunctionsGR,findOverlapAsClusters)
 importFrom(usefulLDfunctionsGR,narrowPeakDFFromGR)
 importFrom(utils,head)
+importFrom(utils,write.table)