Ranch

DESCRIPTION

@@ -28,7 +28,7 @@ NeedsCompilation: no
 Author: Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut],
     Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith
     [aut]
-Collate:
+Collate: 
     'AllGenerics.R'
     'Clinical-class.R'
     'GMS_Virtual-class.R'
@@ -45,9 +45,16 @@ Collate:
     'MutationAnnotationFormat_v2.3-class.R'
     'MutationAnnotationFormat_v2.4-class.R'
     'Rainfall-class.R'
+    'StructuralVariant-class.R'
+    'VCF_Virtual-class.R'
+    'VCF_Manta_v4.1-class.R'
+    'VCF_Manta_v4.2-class.R'
     'VEP_Virtual-class.R'
     'VEP-class.R'
     'VEP_v88-class.R'
+    'VarScanFormat_Virtual-class.R'
+    'VarScanFormat-class.R'
+    'VariantCallFormat-class.R'
     'Waterfall-class.R'
     'cnFreq.R'
     'cnFreq_buildMain.R'
@@ -59,6 +66,7 @@ Collate:
     'cnView.R'
     'cnView_buildMain.R'
     'cnView_qual.R'
+    'combinedCnLoh-class.R'
     'compIdent.R'
     'compIdent_bamRcnt.R'
     'compIdent_bamRcnt_qual.R'
@@ -67,6 +75,7 @@ Collate:
     'covBars.R'
     'covBars_buildMain.R'
     'covBars_qual.R'
+    'deprecated-lohSpec.R'
     'deprecated.R'
     'genCov.R'
     'genCov_alignPlot.R'
@@ -96,17 +105,7 @@ Collate:
     'ideoView_buildMain.R'
     'ideoView_formatCytobands.R'
     'ideoView_qual.R'
-    'lohSpec.R'
-    'lohSpec_buildMain.R'
-    'lohSpec_fileGlob.R'
-    'lohSpec_lohCalc.R'
-    'lohSpec_qual.R'
-    'lohSpec_slidingWindow.R'
-    'lohSpec_stepCalc.R'
-    'lohSpec_tileCalc.R'
-    'lohSpec_tilePosition.R'
-    'lohSpec_tileWindow.R'
-    'lohSpec_windowPosition.R'
+    'lohSpec-class.R'
     'lohView.R'
     'lohView_buildMain.R'
     'lohView_qual.R'

NAMESPACE

@@ -2,13 +2,18 @@
 
 export(Clinical)
 export(GMS)
+export(LohSpec)
 export(MutSpectra)
 export(MutationAnnotationFormat)
 export(Rainfall)
+export(StructuralVariant)
 export(TvTi)
 export(VEP)
+export(VarScanFormat)
+export(VariantCallFormat)
 export(Waterfall)
 export(cnFreq)
+export(cnLoh)
 export(cnSpec)
 export(cnView)
 export(compIdent)
@@ -25,18 +30,24 @@ exportClasses(GMS)
 exportClasses(MutSpectra)
 exportClasses(MutationAnnotationFormat)
 exportClasses(Rainfall)
+exportClasses(StructuralVariant)
 exportClasses(VEP)
+exportClasses(VarScanFormat)
 exportClasses(Waterfall)
+exportClasses(cnLoh)
+exportClasses(lohSpec)
 exportMethods(drawPlot)
 exportMethods(getData)
 exportMethods(getDescription)
 exportMethods(getGrob)
 exportMethods(getHeader)
+exportMethods(getLohData)
 exportMethods(getMeta)
 exportMethods(getMutation)
 exportMethods(getPath)
 exportMethods(getPosition)
 exportMethods(getSample)
+exportMethods(getVarScan)
 exportMethods(getVersion)
 exportMethods(writeData)
 import(data.table)
@@ -90,6 +101,7 @@ importFrom(data.table,is.data.table)
 importFrom(data.table,melt)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
+importFrom(ggforce,geom_bezier)
 importFrom(ggplot2,ggplotGrob)
 importFrom(grDevices,colors)
 importFrom(grid,grid.draw)
@@ -102,6 +114,8 @@ importFrom(gtable,gtable)
 importFrom(gtable,gtable_add_grob)
 importFrom(gtable,gtable_add_rows)
 importFrom(gtools,mixedsort)
+importFrom(karyoploteR,getCytobandColors)
+importFrom(karyoploteR,getCytobands)
 importFrom(plyr,adply)
 importFrom(plyr,count)
 importFrom(plyr,ldply)