## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------ BiocStyle::latex() ## ----rbioc-pdata, echo=FALSE--------------------------------------------- pdataFile <- system.file(package="BiocIntro", "extdata", "pData.csv") ## ----rbioc-pdata-user, eval=FALSE---------------------------------------- ## pdataFile <- "~/extdata/pData.csv" ## ----file-exists--------------------------------------------------------- stopifnot(file.exists(pdataFile)) ## ----rbioc-pdata-csv----------------------------------------------------- pdata <- read.table(pdataFile) dim(pdata) names(pdata) summary(pdata) ## ----rbioc-pdata-summarize----------------------------------------------- head(pdata[,"sex"], 3) head(pdata$sex, 3) head(pdata[["sex"]], 3) sapply(pdata, class) ## ----rbioc-pdata-sextab-------------------------------------------------- table(pdata$sex, useNA="ifany") ## ----rbioc-pdata-molbiol------------------------------------------------- with(pdata, table(mol.biol, useNA="ifany")) ## ----rbbioc-pdata-bcrabl------------------------------------------------- ridx <- pdata$mol.biol %in% c("BCR/ABL", "NEG") ## ----rbioc-pdata-molbiol-selected---------------------------------------- table(ridx) sum(ridx) ## ----rbioc-pdata-subset-------------------------------------------------- pdata1 <- pdata[ridx,] ## ----rbioc-pdata-subset-levels------------------------------------------- levels(pdata1$mol.biol) ## ----rbioc-pdata-subset-recode------------------------------------------- pdata1$mol.biol <- factor(pdata1$mol.biol) table(pdata1$mol.biol) ## ----rbioc-pdata-age-molbiol--------------------------------------------- with(pdata1, t.test(age ~ mol.biol)) ## ----rbioc-pdata-boxplot, eval=FALSE------------------------------------- ## ## not evaluated ## boxplot(age ~ mol.biol, pdata1)