## ----风格，echo = false，结果='Asis'-----------------------------------------------------生物焦质:: markdown（）选项（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”）））## ----设置，echo = false，消息= false，警告= false -------------------------------------- suppressPackageStartUpMessages（{图书馆（Airway）库（Deseq2）库（GGPlot2）库（org.hs.eg.db）}）## ----配置 - 测试-------------------------------------------------------------------------------------------- Stopifnot（getRversion（）> ='3.2'&& getRversion（）<'3.3'，Biocinstaller :: biocversion（）==“3.2”）## ----气道 - 概要化---------------------------------------------------------------------------------------------------------图书馆（Airway）＃'experimentData'包......数据（Airway）＃...使用样本数据集..。Airway＃......这是一个概括的医疗头（测定（气道））＃包含一个计数头的矩阵（Rowranges（airwAY））＃有关基因的信息...... CONGATA（AIRWAY）[，1：3]＃......以及样本##协调子集UNTRT < - AIRWAY [，AIRWAY $ DEX =='UNTRT']头（测定）头部（UNTTT））Coldata（UNTTT）[，1：3] ## ---- Airway-Coldata ---------------------------------------------------------------------------------------------- 图书馆（Airway）＃'实验室'套餐......数据（Airway）＃...使用样品数据集... CONGATA（AIRWAY）[，1：3]＃...代表概要##----气道测定-------------------------------------------------------------------------- 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()