## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----fig.width=7, fig.height=4, echo=FALSE------------------------------------ load('../data/binnedDeltaPlot.rda') print(binnedDeltaPlot) ## ----message=FALSE------------------------------------------------------------ library(deltaCaptureC) significantRegionsPlot = plotSignificantRegions(significantRegions, significanceType, plotTitle) ## ----fig.width=7, fig.height=4, echo=FALSE------------------------------------ load('../data/significantRegionsPlot.rda') significantRegionsPlot = significantRegionsPlot + ggplot2::theme(axis.text=ggplot2::element_text(size=8)) print(significantRegionsPlot) ## ----message=FALSE------------------------------------------------------------ library(SummarizedExperiment) library(deltaCaptureC) se = miniSE counts = assays(se)[['counts']] sizeFactors = DESeq2::estimateSizeFactorsForMatrix(counts) colData(se)$sizeFactors = sizeFactors assays(se)[['normalizedCounts']] = counts for(i in seq_len(ncol(assays(se)[['normalizedCounts']]))) { assays(se)[['normalizedCounts']][,i] = assays(se)[['normalizedCounts']][,i] / colData(se)$sizeFactors[i] } ## ----message=FALSE------------------------------------------------------------ library(SummarizedExperiment) library(deltaCaptureC) meanNormalizedCountsSE = getMeanNormalizedCountsSE(miniSE) meanCounts = assay(meanNormalizedCountsSE) delta = matrix(meanCounts[,1] - meanCounts[,2],ncol=1) colData = data.frame(delta=sprintf('%s - %s', as.character(colData(meanNormalizedCountsSE)$treatment[1]), as.character(colData(meanNormalizedCountsSE)$treatment[2])), stringsAsFactors=FALSE) deltaSE = SummarizedExperiment(assay=list(delta=delta), colData=colData) rowRanges(deltaSE) = rowRanges(meanNormalizedCountsSE) ## ----message=FALSE------------------------------------------------------------ library(deltaCaptureC) print(length(smallSetOfSmallBins)) print(length(smallerDeltaSE)) tictoc::tic('binning into small bins') binnedSummarizedExperiment = binSummarizedExperiment(smallSetOfSmallBins,smallerDeltaSE) tictoc::toc() ## ----message=FALSE------------------------------------------------------------ library(deltaCaptureC) tictoc::tic('rebinning to larger bin size') rebinnedSummarizedExperiment = rebinToMultiple(binnedSummarizedExperiment,10) tictoc::toc()