## ----eval=FALSE--------------------------------------------------------------- # #ALIGN: # sample.fastq -> sample.sam # #CONVERT: # samtools view -b -S sample.sam -o sample.bam # #SORT: # samtools sort sample.bam sample_sorted # #INDEXING: # samtools index sample_sorted.bam ## ----eval=TRUE---------------------------------------------------------------- library(wavClusteR) filename <- system.file( "extdata", "example.bam", package = "wavClusteR" ) Bam <- readSortedBam(filename = filename) Bam ## ----eval=TRUE---------------------------------------------------------------- countTable <- getAllSub( Bam, minCov = 10 ) head( countTable ) ## ----fig.width=5, fig.height=5, fig.align='center', eval=TRUE----------------- plotSubstitutions( countTable, highlight = "TC" ) ## ----eval=FALSE--------------------------------------------------------------- # model <- fitMixtureModel(countTable, substitution = "TC") ## ----eval=TRUE---------------------------------------------------------------- data(model) str(model) ## ----fig.width=7, fig.height=4.5, fig.align='center', eval=TRUE--------------- (support <- getExpInterval( model, bayes = TRUE ) ) ## ----fig.width=7, fig.height=4.5, fig.align='center', eval=TRUE--------------- (support <- getExpInterval( model, bayes = FALSE, leftProb = 0.9, rightProb = 0.9 ) ) ## ----fig.width=7, fig.height=5, fig.align='center', eval=TRUE----------------- plotSubstitutions( countTable, highlight = "TC", model ) ## ----eval=TRUE---------------------------------------------------------------- highConfSub <- getHighConfSub( countTable, support = support, substitution = "TC" ) head( highConfSub ) ## ----eval=FALSE--------------------------------------------------------------- # highConfSub <- getHighConfSub( countTable, # supportStart = 0.2, # supportEnd = 0.7, # substitution = "TC" ) # head( highConfSub ) ## ----eval=TRUE---------------------------------------------------------------- coverage <- coverage( Bam ) coverage$chrX ## ----eval=TRUE---------------------------------------------------------------- clusters <- getClusters( highConfSub = highConfSub, coverage = coverage, sortedBam = Bam, threshold = 1, cores = 1 ) clusters ## ----eval=TRUE---------------------------------------------------------------- clusters <- getClusters( highConfSub = highConfSub, coverage = coverage, sortedBam = Bam, cores = 1 ) clusters ## ----eval=TRUE---------------------------------------------------------------- require(BSgenome.Hsapiens.UCSC.hg19) wavclusters <- filterClusters( clusters = clusters, highConfSub = highConfSub, coverage = coverage, model = model, genome = Hsapiens, refBase = "T", minWidth = 12) wavclusters ## ----eval=FALSE--------------------------------------------------------------- # exportHighConfSub( highConfSub = highConfSub, # filename = "hcTC.bed", # trackname = "hcTC", # description = "hcTC" ) ## ----eval=FALSE--------------------------------------------------------------- # exportClusters( clusters = wavclusters, # filename = "wavClusters.bed", # trackname = "wavClusters", # description = "wavClusters" ) ## ----eval=FALSE--------------------------------------------------------------- # exportCoverage( coverage = coverage, filename = "coverage.bigWig" ) ## ----eval=FALSE--------------------------------------------------------------- # txDB <- makeTxDbFromUCSC(genome = "hg19", tablename = "ensGene") ## ----eval=FALSE--------------------------------------------------------------- # annotateClusters( clusters = wavclusters, # txDB = txDB, # plot = TRUE, # verbose = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # getMetaGene( clusters = wavclusters, # txDB = txDB, # upstream = 1e3, # downstream = 1e3, # nBins = 40, # nBinsUD = 10, # minLength = 1, # plot = TRUE, # verbose = TRUE ) ## ----eval=FALSE--------------------------------------------------------------- # getMetaTSS( sortedBam = Bam, # txDB = txDB, # upstream = 1e3, # downstream = 1e3, # nBins = 40, # unique = FALSE, # plot = TRUE, # verbose = TRUE ) ## ----fig.width=5, fig.height=5, fig.align='center', eval=TRUE----------------- plotSizeDistribution( clusters = wavclusters, showCov = TRUE, col = "skyblue2" ) ## ----fig.width=5, fig.height=5, fig.align='center', eval=FALSE---------------- # plotStatistics( clusters = wavclusters, # corMethod = "spearman", # lower = panel.smooth ) ## ----eval=TRUE---------------------------------------------------------------- sessionInfo()