## ----style, echo = FALSE, results = 'asis'---------------------------------
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))

## ----echo=FALSE------------------------------------------------------------
path <- system.file(package="BiocIntro", "extdata", "BRFSS-subset.csv")

## ----ALL-choose, eval=FALSE------------------------------------------------
#  path <- file.choose()    # look for BRFSS-subset.csv

## ----ALL-input-------------------------------------------------------------
stopifnot(file.exists(path))
brfss <- read.csv(path)

## --------------------------------------------------------------------------
names(brfss)
median(brfss$Age)

## ----brfss-anyNA-----------------------------------------------------------
any(is.na(brfss$Age))
anyNA(brfss$Age)        # same, but more efficient

## --------------------------------------------------------------------------
median(brfss$Age, na.rm=TRUE)

## ---- eval=FALSE-----------------------------------------------------------
#  plot(brfss$age)
#  plot(sort(brfss$age))
#  sortedAge = sort(brfss$age)
#  ?plot

## --------------------------------------------------------------------------
summary(brfss)
brfss$Year <- factor(brfss$Year)

## --------------------------------------------------------------------------
brfssFemale <- brfss[brfss$Sex == "Female",]
summary(brfssFemale)

## --------------------------------------------------------------------------
plot(Weight ~ Year, brfssFemale)

## --------------------------------------------------------------------------
t.test(Weight ~ Year, brfssFemale)

## --------------------------------------------------------------------------
brfss2010Male <- subset(brfss,  Year == 2010 & Sex == "Male")
summary(brfss2010Male)

## --------------------------------------------------------------------------
hist(brfss2010Male$Weight)
hist(brfss2010Male$Height)
plot(Weight ~ Height, brfss2010Male)

## --------------------------------------------------------------------------
fit <- lm(Weight ~ Height, brfss2010Male)
fit

## --------------------------------------------------------------------------
anova(fit)


## --------------------------------------------------------------------------
plot(Weight ~ Height, brfss2010Male)
abline(fit, col="blue", lwd=2)
points(180, 88, col="red", cex=4, pch=20)

## ---- eval=FALSE-----------------------------------------------------------
#  class(fit)                 # 'noun'
#  methods(class=class(fit))  # 'verb'

## ---- eval=FALSE-----------------------------------------------------------
#  plot(fit)
#  ?plot.lm

## ----echo=FALSE------------------------------------------------------------
path <- system.file(package="BiocIntro", "extdata", "ALL-expression.csv")

## ----ALL-choose-again, eval=FALSE------------------------------------------
#  path <- file.choose()          # look for ALL-expression.csv
#  stopifnot(file.exists(path))

## ----ALL-input-exprs-------------------------------------------------------
exprs <- read.csv(path, row.names=1, check.names=FALSE)
exprs <- as.matrix(exprs)
class(exprs)
dim(exprs)
exprs[1:6, 1:10]
range(exprs)

## ----echo=FALSE------------------------------------------------------------
path <- system.file(package="BiocIntro", "extdata", "ALL-phenoData.csv")

## ----ALL-phenoData.csv-clustering-student, eval=FALSE----------------------
#  path <- file.choose()         # look for ALL-phenoData.csv
#  stopifnot(file.exists(path))

## --------------------------------------------------------------------------
pdata <- read.csv(path, row.names=1)
class(pdata)
dim(pdata)
head(pdata)

## ----colors----------------------------------------------------------------
library(RColorBrewer)  ## not available? install package via RStudio
highlight <- brewer.pal(3, "Set2")[1:2]

## ----ALL-BorT--------------------------------------------------------------
pdata$BorT <- factor(substr(pdata$BT, 1, 1))

## --------------------------------------------------------------------------
exprs <- t(exprs)

## --------------------------------------------------------------------------
stopifnot(identical(rownames(pdata), rownames(exprs)))

## --------------------------------------------------------------------------
d <- dist(exprs)

## --------------------------------------------------------------------------
cmd <- cmdscale(d)

## --------------------------------------------------------------------------
plot(cmd, col=highlight[pdata$BorT])