## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("scmeth") ## ---- warning=FALSE, message=FALSE-------------------------------------------- library(scmeth) ## ---- eval=FALSE-------------------------------------------------------------- # directory <- system.file("extdata", "bismark_data", package='scmeth') # bsObject <- HDF5Array::loadHDF5SummarizedExperiment(directory) ## ---- eval=FALSE-------------------------------------------------------------- # report(bsObject, '~/Documents', Hsapiens, "hg38") ## ---- warning=FALSE, message=FALSE, comment=FALSE---------------------------- directory <- system.file("extdata", "bismark_data", package='scmeth') bsObject <- HDF5Array::loadHDF5SummarizedExperiment(directory) ## ----------------------------------------------------------------------------- scmeth::coverage(bsObject) ## ---- fig.width=6, fig.height=3----------------------------------------------- readmetrics(bsObject) ## ---- warning=FALSE, message=FALSE-------------------------------------------- library(BSgenome.Mmusculus.UCSC.mm10) load(system.file("extdata", 'bsObject.rda', package='scmeth')) repMask(bs, Mmusculus, "mm10") ## ---- warning=FALSE----------------------------------------------------------- chromosomeCoverage(bsObject) ## ---- warning=FALSE,message=FALSE--------------------------------------------- #library(annotatr) featureList <- c('cpg_islands', 'cpg_shores', 'cpg_shelves') DT::datatable(featureCoverage(bsObject, features=featureList, "hg38")) ## ---- warning=FALSE, message=FALSE-------------------------------------------- library(BSgenome.Hsapiens.NCBI.GRCh38) DT::datatable(cpgDensity(bsObject, Hsapiens, windowLength=1000, small=TRUE)) ## ----warning=FALSE------------------------------------------------------------ DT::datatable(scmeth::downsample(bsObject)) ## ---- warning=FALSE, message=FALSE, fig.width=6, fig.height=6----------------- methylationBiasFile <- '2017-04-21_HG23KBCXY_2_AGGCAGAA_TATCTC_pe.M-bias.txt' mbiasList <- mbiasplot(mbiasFiles=system.file("extdata", methylationBiasFile, package='scmeth')) mbiasDf <- do.call(rbind.data.frame, mbiasList) meanTable <- stats::aggregate(methylation ~ position + read, data=mbiasDf, FUN=mean) sdTable <- stats::aggregate(methylation ~ position + read, data=mbiasDf, FUN=sd) seTable <- stats::aggregate(methylation ~ position + read, data=mbiasDf, FUN=function(x){sd(x)/sqrt(length(x))}) sum_mt<-data.frame('position'=meanTable$position,'read'=meanTable$read, 'meth'=meanTable$methylation, 'sdMeth'=sdTable$methylation, 'seMeth'=seTable$methylation) sum_mt$upperCI <- sum_mt$meth + (1.96*sum_mt$seMeth) sum_mt$lowerCI <- sum_mt$meth - (1.96*sum_mt$seMeth) sum_mt$read_rep <- paste(sum_mt$read, sum_mt$position, sep="_") g <- ggplot2::ggplot(sum_mt) g <- g + ggplot2::geom_line(ggplot2::aes_string(x='position', y='meth', colour='read')) g <- g + ggplot2::geom_ribbon(ggplot2::aes_string(ymin = 'lowerCI', ymax = 'upperCI', x='position', fill = 'read'), alpha=0.4) g <- g + ggplot2::ylim(0,100) + ggplot2::ggtitle('Mbias Plot') g <- g + ggplot2::ylab('methylation') g ## ---- warning=FALSE, message=FALSE, fig.width=6, fig.height=3----------------- methylationDist(bsObject) ## ---- warning=FALSE, message=FALSE, fig.width=4, fig.height=6----------------- bsConversionPlot(bsObject) ## ---- warning=FALSE, message=FALSE-------------------------------------------- sessionInfo()