## ----style-Sweave, eval=TRUE, echo=FALSE, results='asis'----------------- BiocStyle::latex() ## ----quickstart,message=FALSE,eval=FALSE--------------------------------- ## ## library('MMDiff2') ## library('MMDiffBamSubset') ## ExperimentData <- list(genome='BSgenome.Mmusculus.UCSC.mm9', ## dataDir=system.file("extdata", package="MMDiffBamSubset"), ## sampleSheet="Cfp1.csv") ## MetaData <- list('ExpData' = ExperimentData) ## MMD <- DBAmmd(MetaData) ## data("Cfp1-Peaks") ## MMD <- setRegions(MMD,Peaks) ## MMD <- getPeakReads(MMD) ## MMD <- estimateFragmentCenters(MMD) ## MMD <- compHists(MMD) ## MMD <- compDists(MMD) ## MMD <- setContrast(MMD,contrast='byCondition') ## MMD <- compPvals(MMD) ## res <- reportResults(MMD) ## ----setup,message=FALSE------------------------------------------------- # load software package library('MMDiff2') ## ----dataload,message=FALSE---------------------------------------------- # load data packages library('MMDiffBamSubset') # create metaData: ExperimentData <- list(genome = 'BSgenome.Mmusculus.UCSC.mm9', dataDir = system.file("extdata", package="MMDiffBamSubset"), sampleSheet="Cfp1.csv") MetaData <- list('ExpData' = ExperimentData) ## ----regions,message=FALSE----------------------------------------------- data('Cfp1-Peaks') MMD <- DBAmmd(MetaData) MMD <- setRegions(MMD,Peaks) MMD <- getPeakReads(MMD) ## ----fragC, message=FALSE, markup='hide'--------------------------------- MMD <- estimateFragmentCenters(MMD) ## ----hists,message=FALSE------------------------------------------------- MMD <- compHists(MMD, bin.length=20, whichPos="Center") ## ----peakplot1, markup='hide', message=FALSE, fig.width=7, fig.height=3, fig.align='center'---- plotPeak(MMD, Peak.id='241', plot.input = FALSE, whichPos="Center") ## ----motif specifcation-------------------------------------------------- library('MotifDb') motifs <- query(query(MotifDb, 'Mmusculus'), 'E2F') ## ----peakplot2,message=FALSE,fig.width=7, fig.height=4, fig.align='center'---- plotPeak(MMD, Peak.id='241', NormMethod=NULL,plot.input = FALSE,whichPos="Center", Motifs=motifs,Motifcutoff="80%") ## ----peakplot3,message=FALSE,fig.width=7, fig.height=5, fig.align='center'---- data("mm9-Genes") names(GR) <- GR$tx_name GR <- list(UCSCKnownGenes = GR) plotPeak(MMD, Peak.id='241', NormMethod=NULL,plot.input = FALSE, whichPos="Center",Motifs=motifs, anno=GR) ## ----dists, message=FALSE, include=FALSE--------------------------------- MMD <- compDists(MMD, dist.method = "MMD", run.parallel = FALSE) ## ----contrast------------------------------------------------------------ MMD <- setContrast(MMD,contrast='byCondition') ## ----contrast2,message=FALSE, include=FALSE------------------------------ group1 <- Samples(MMD)$Condition=='1' names(group1) <- Samples(MMD)$SampleID group2 <- Samples(MMD)$Condition=='2' names(group2) <- Samples(MMD)$SampleID contrast <- list(group1=group1, group2=group2, name1='WT,REsc', name2='Null') #setContrast(MMD,contrast=contrast) ## ----diffTest------------------------------------------------------------ MMD <- compPvals(MMD,dist.method='MMD') ## ------------------------------------------------------------------------ plotDists(MMD, dist.method='MMD',whichContrast=1, diff.method='MMD.locfit', bUsePval=FALSE, th=0.1, title=NULL, what=3, xlim=NULL,ylim=NULL,Peak.IDs=NULL, withLegend=TRUE) ## ------------------------------------------------------------------------ res <- reportResults(MMD) Peak.ids <- names(res) plotPeak(MMD, Peak.id=Peak.ids[1], NormMethod=NULL,plot.input = FALSE, whichPos="Center",Motifs=motifs, anno=GR,whichContrast = 1) dev.off() plotDISTS4Peak(MMD,Peak.id=Peak.ids[1],dist.method='MMD', whichContrast=1,Zoom=TRUE) ## ----shinyApp,eval=FALSE------------------------------------------------- ## runShinyMMDiff2(MMD) ## ------------------------------------------------------------------------ sessionInfo()