## ----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")))

## --------------------------------------------------------------------------
1 + 2
x = c(1, 2, 3)
1:3             # sequence of integers from 1 to 3
x + c(4, 5, 6)  # vectorized
x + 4           # recycling

## --------------------------------------------------------------------------
x = rnorm(100)
y = x + rnorm(100)
plot(x, y)

## --------------------------------------------------------------------------
df <- data.frame(Independent = x, Dependent = y)
head(df)
df[1:5, 1:2]
df[1:5, ]
plot(Dependent ~ Independent, df)  # 'formula' interface

## --------------------------------------------------------------------------
ridx <- (df$Dependent > 0) & (df$Independent > 0)

## --------------------------------------------------------------------------
plot(Dependent ~ Independent, df[ridx, ])

## --------------------------------------------------------------------------
plot(
    Dependent ~ Independent, df,
    subset = (Dependent > 0) & (Independent > 0)
)

## --------------------------------------------------------------------------
fit <- lm(Dependent ~ Independent, df)  # linear model -- regression
anova(fit)                              # summary table
plot(Dependent ~ Independent, df)
abline(fit)

## --------------------------------------------------------------------------
class(fit)
methods(class="lm")

## ---- eval=FALSE-----------------------------------------------------------
#  ?"plot"          # plain-old-function or generic
#  ?"plot.formula"  # method
#  ?"plot.lm"       # method for object of class 'lm', plot(fit)

## --------------------------------------------------------------------------
library(ggplot2)
ggplot(df, aes(x = Independent, y = Dependent)) +
    geom_point() + geom_smooth(method = "lm")

## ---- message = FALSE------------------------------------------------------
library(Biostrings)
dna <- DNAStringSet(c("AACTCC", "CTGCA"))
dna
reverseComplement(dna)

## --------------------------------------------------------------------------
sessionInfo()