## ----style, echo = FALSE, results = 'asis'-------------------------------------------------------- BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))) ## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE-------------------------------------------- suppressPackageStartupMessages({ library(airway) library(DESeq2) library(ggplot2) library(org.Hs.eg.db) }) ## ----configure-test------------------------------------------------------------------------------- stopifnot( getRversion() >= '3.2' && getRversion() < '3.3', BiocInstaller::biocVersion() == "3.2" ) ## ----airway-SummarizedExperiment------------------------------------------------------------------ library(airway) # An 'ExperimentData' package... data(airway) # ...with a sample data set... airway # ...that is a SummarizedExperiment head(assay(airway)) # contains a matrix of counts head(rowRanges(airway)) # information about the genes... colData(airway)[, 1:3] # ...and samples ## coordinated subsetting untrt <- airway[, airway$dex == 'untrt'] head(assay(untrt)) colData(untrt)[, 1:3] ## ----airway-colData------------------------------------------------------------------------------- library(airway) # An 'ExperimentData' package... data(airway) # ...with a sample data set... colData(airway)[, 1:3] # ...represented as a SummarizedExperiment ## ----airway-assay--------------------------------------------------------------------------------- head(assay(airway)) ## ----airway-toptable------------------------------------------------------------------------------ library(DESeq2) # package implementing statistical methods dds <- # data and experimental design DESeqDataSet(airway, design = ~ cell + dex) dds <- DESeq(dds) # initial analysis res <- results(dds) # summary results ridx <- # order from largest to smallest absolute log fold change order(abs(res$log2FoldChange), decreasing=TRUE) res <- res[ridx,] head(res) # top-table ## ----airway-viz----------------------------------------------------------------------------------- library(ggplot2) ggplot(as.data.frame(res), aes(x=log2FoldChange, y=-10 * log10(pvalue))) + geom_point() ## ----airway-mapids-------------------------------------------------------------------------------- library(org.Hs.eg.db) ensid <- head(rownames(res)) select(org.Hs.eg.db, ensid, c("SYMBOL", "GENENAME"), "ENSEMBL") ## ----shiny-BAMSpector, eval=FALSE----------------------------------------------------------------- # app <- system.file(package="BiocUruguay2015", "BAMSpector") # shiny::runApp(app) ## ----shiny-MAPlotExplorer, eval=FALSE------------------------------------------------------------- # app <- system.file(package="BiocUruguay2015", "MAPlotExplorer") # shiny::runApp(app) ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()