hg38: non-internet access and plot function export

- Allow retrieval of Seqinfo from local BSgenome files if present. This
  avoids needing an internet connection through Seqinfo, which uses
  fetchExtendedChromInfoFromUCSC under the covers.
- Export plotIdiogram.hg38 for use in TitanCNA.R script

NAMESPACE

@@ -4,7 +4,7 @@ export(loadAlleleCounts,loadDefaultParameters,
 		filterData,getPositionOverlap,wigToRangedData,
 		outputTitanResults,outputModelParameters,correctReadDepth,
 		runEMclonalCN, viterbiClonalCN,computeSDbwIndex,
-		plotAllelicRatio,plotClonalFrequency,plotCNlogRByChr,
+		plotAllelicRatio,plotClonalFrequency,plotCNlogRByChr, plotIdiogram.hg38,
 		plotSubcloneProfiles, outputTitanSegments,
 		setGenomeStyle,plotSegmentMedians,
 		loadHaplotypeAlleleCounts,plotHaplotypeFraction, getHaplotypesFromVCF,

scripts/R_scripts/titanCNA.R

@@ -181,7 +181,12 @@ if (is.null(outplot)){
 dir.create(outplot, showWarnings=verbose)
 outImage <- gsub(".titan.txt", ".RData", outfile)
 
-seqinfo <- Seqinfo(genome=genomeBuild)
+bsg <- paste0("BSgenome.Hsapiens.UCSC.", genomeBuild)
+if (!require(bsg, character.only=TRUE, quietly=TRUE, warn.conflicts=FALSE)) {
+	seqinfo <- Seqinfo(genome=genomeBuild)
+} else {
+	seqinfo <- seqinfo(get(bsg))
+}
 seqlevelsStyle(chrs) <- genomeStyle
 ## exclude chrX if gender==male ##
 if (gender == "male" || gender == "Male" || gender == "MALE"){