## ----style, echo = FALSE, results = 'asis'-------------------------------------------------------- BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))) ## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE-------------------------------------------- suppressPackageStartupMessages({ library(ALL) library(airway) }) ## ----configure-test------------------------------------------------------------------------------- stopifnot( getRversion() >= '3.2' && getRversion() < '3.3', BiocInstaller::biocVersion() == "3.2" ) ## ----read.table----------------------------------------------------------------------------------- fname = "ALLphenoData.tsv" ## use file.choose() to find the file pdata = read.table(fname) ## ----ALL-properties------------------------------------------------------------------------------- class(pdata) colnames(pdata) dim(pdata) head(pdata) summary(pdata$sex) summary(pdata$cyto.normal) ## ----ALL-subset----------------------------------------------------------------------------------- pdata[1:5, 3:4] pdata[1:5, ] head(pdata[, 3:5]) tail(pdata[, 3:5], 3) head(pdata$age) head(pdata$sex) head(pdata[pdata$age > 21,]) ## ----exprs---------------------------------------------------------------------------------------- fname <- "ALLassay.tsv" exprs <- as.matrix(read.table(fname, check.names=FALSE)) ## ----SummarizedExperiment------------------------------------------------------------------------- if (BiocInstaller::biocVersion() >= "3.2") { library(SummarizedExperiment) } else { library(GenomicRanges) } ## ----make-SE-------------------------------------------------------------------------------------- se <- SummarizedExperiment(exprs, colData=DataFrame(pdata)) ## ----se-ops--------------------------------------------------------------------------------------- head(colData(se)) assay(se)[1:5, 1:5] se$sex %in% "M" males <- se[,se$sex %in% "M"] males assay(males)[1:5, 1:5] ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()