--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.R	Fri May 01 05:41:51 2015 -0400
@@ -0,0 +1,34 @@
+library(riboSeqR)
+fastaCDS_REF <- findCDS(fastaFile='rsem_chlamy236_deNovo.transcripts.fa', startCodon=c("ATG"), stopCodon=c("TAG", "TAA", "TGA"))
+ribofiles <- paste("chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
+rnafiles <- paste("chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
+riboDat_REF <- readRibodata(ribofiles, rnafiles, replicates=c("WT", "WT", "M", "M"))
+fCs_REF <- frameCounting(riboDat_REF, fastaCDS_REF)
+fS_REF <- readingFrame(rC = fCs_REF)
+
+pdf(file="/tmp/Periodicity-plot.pdf")
+plotFS(fS_REF, legend.text = c('Frame 0', 'Frame 1', 'Frame 2'))
+dev.off()
+
+ffCs_REF <- filterHits(fCs_REF, lengths=c(27,28), frames=list(1,0), hitMean = 50, unqhitMean = 10, fS=fS_REF)
+pdf(file='/tmp/Metagene-analysis-plot.pdf')
+plotCDS(coordinates=ffCs_REF@CDS, riboDat=riboDat_REF, lengths=27)
+plotCDS(coordinates=ffCs_REF@CDS, riboDat=riboDat_REF, lengths=28)
+dev.off()
+
+pdf(file='/tmp/Ribosome-profile-plot.pdf')
+plotTranscript("CUFF.37930.1", coordinates=ffCs_REF@CDS, riboData=riboDat_REF, length=27, cap=200)
+dev.off()
+
+riboCounts_REF <- sliceCounts(ffCs_REF, lengths = c(27,28), frames = list(0,2))
+rnaCounts_REF <- rnaCounts(riboDat_REF, ffCs_REF@CDS)
+
+save('fastaCDS_REF', 'riboDat_REF', 'fCs_REF', 'fS_REF', 'ffCs_REF', 'riboCounts_REF', 'rnaCounts_REF', file='Robjects.rda')
+
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