## ----1--------------------------------------------------------------------- library(cleanUpdTSeq) testFile <- system.file("extdata", "test.bed", package="cleanUpdTSeq") testSet <- read.table(testFile, sep="\t", header=TRUE) peaks <- BED2GRangesSeq(testSet, withSeq=FALSE) ## ----2--------------------------------------------------------------------- peaks <- BED2GRangesSeq(testSet, upstream.seq.ind=7, downstream.seq.ind=8, withSeq=TRUE) ## ----3--------------------------------------------------------------------- head(testSet) ## ----4--------------------------------------------------------------------- library(BSgenome.Drerio.UCSC.danRer7) testSet.NaiveBayes <- buildFeatureVector(peaks, BSgenomeName=Drerio, upstream=40, downstream=30, wordSize=6, alphabet=c("ACGT"), sampleType="unknown", replaceNAdistance=30, method="NaiveBayes", ZeroBasedIndex=1, fetchSeq=TRUE) ## ----5--------------------------------------------------------------------- data(data.NaiveBayes) if(interactive()){ predictTestSet(data.NaiveBayes$Negative, data.NaiveBayes$Positive, testSet.NaiveBayes=testSet.NaiveBayes, outputFile="test-predNaiveBayes.tsv", assignmentCutoff=0.5) } ## ----6--------------------------------------------------------------------- data(classifier) testResults <- predictTestSet(testSet.NaiveBayes=testSet.NaiveBayes, classifier=classifier, outputFile=NULL, assignmentCutoff=0.5) head(testResults) ## ----sessionInfo, results='asis'------------------------------------------- sessionInfo()