1. 1 R Programming Zhi Wei

2. 2 Language layout  Three types of statement expression: it is evaluated, printed, and the value is lost (3+5) assignment: passes the value to a variable but the result is not printed automatically (out<- 3+5) comment: (#This is a comment)

3. 3 Loops and conditionals  Conditional if (expr) expr if (expr) expr else expr  Iteration repeat expr while (expr) expr for (name in expr1) expr  For comparisons use: equal: == not equal: != greater/less than: > < greater/less than or equal: >= <= NOT, AND, OR: !, &, |

4. 4 Examples  What does the following code do? if (value==1) {check<-1} else {check<-0} counter<-0 for (i in 1:10) { if (geneExpr[i,2]<10){counter<-counter+1} } counter=sum(geneExpr[c(1:10),2]<10)

5. Accessing a data frame with logical vector data set ewr (UsingR package) >attach(ewr) >boxplot(ewr[inorout=="in", 3:10], main="Taxi in") >detach(ewr)  subset() function new.df = subset(old.df, subset=…, select=…) ewr.in = subset(ewr, subset= inorout=="in", select=3:10) ewr.out = subset(ewr, subset= inorout=="out", select=3:10) 5

6. Sorting a data frame by one of its column >attach(mtcars) >mtcars[order(mpg),] >mtcars[order(mpg, decreasing=T),] >mtcars[order(cyl,hp),] 6

7. Vectorization: avoid Loop (page 26, supp. R book, moodle has a copy)  apply(X, MARGIN, FUN,...) find minimum values of each row of matrix m  m <- matrix(rnorm(100), ncol=4)  apply(m, 2, min) ##- function with extra args:  myMin cut]) }  apply(m,2, myMin, cut=0)  lapply(X, FUN,...), sapply, tapply lapply(thuesen, mean, na.rm=T) sapply(thuesen, mean, na.rm=T) tapply(energy$expend, energy$stature, median) aggregate(energy$expend, energy["stature"], median) 7

8. Edit and Save your script  Can write many lines of code in any of your favorite text editors and run all at once Simply paste the commands into R Save your script and then Use function source( “ path/yourscript ” ), to run in batch mode the functions/codes saved in file “ yourscript ” (use options(echo=T) to have the commands echoed) 8