Appendix V. R Basics
How to make professional and beautiful plots
Tips:
Do things with multiple ways
Efficient Writing: Bash > R > Perl/Python > Excel > C,C++
1. Install and Use R
a. Install R
See the official site of R: https://www.r-project.org/ （Docker中已经安装好）
Here is an example of installation in Linux:
For CentOS
yum -y install epel-release yum -y install RFor Ubuntu
apt -y install r-base
b. Install RStudio
If you like a nice interface to use R instead of Linux command line, you can try RStudio: https://www.rstudio.com/
We have some instruction of Rstudio in Appendix. Plot with R
c. Use R
how to enter?
On Mac or Linux, you can open a Terminal and type
ROn Windows or Mac, you can find a program with this logo:
How to quit?
q()How to get help?
?t.test
2. Basic Data Types
> x = 10.5 # assign a decimal value
> x # print the value of x
[1] 10.5
> class(x) # print the class name of x
[1] "numeric"
> y = as.integer(3)
> y # print the value of y
[1] 3
> class(y) # print the class name of y
[1] "integer"
> z = 1 + 2i # create a complex number
> z # print the value of z
[1] 1+2i
> class(z) # print the class name of z
[1] "complex"
> x = 1; y = 2 # sample values
> z = x > y # is x larger than y?
> z # print the logical value
[1] FALSE
> class(z) # print the class name of z
[1] "logical"
> x = as.character(10.5)
> x # print the character string
[1] "10.5"
> class(x) # print the class name of x
[1] "character"
- vector
> c(2, 3, 5)
[1] 2 3 5
> n = c(2, 3, 5)
> s = c("aa", "bb", "cc", "dd", "ee")
> c(n, s)
[1] "2" "3" "5" "aa" "bb" "cc" "dd" "ee"
> s = c("aa", "bb", "cc", "dd", "ee")
> s[3]
[1] "cc"
- matrix
> B = matrix(
+ c(2, 4, 3, 1, 5, 7),
+ nrow=3,
+ ncol=2)
> B # B has 3 rows and 2 columns
[,1] [,2]
[1,] 2 1
[2,] 4 5
[3,] 3 7
- list
> n = c(2, 3, 5)
> s = c("aa", "bb", "cc", "dd", "ee")
> b = c(TRUE, FALSE, TRUE, FALSE, FALSE)
> x = list(n, s, b, 3) # x contains copies of n, s, b
- data frame
> n = c(2, 3, 5)
> s = c("aa", "bb", "cc")
> b = c(TRUE, FALSE, TRUE)
> df = data.frame(n, s, b) # df is a data frame
> df
n s b
1 2 aa TRUE
2 3 bb FALSE
3 5 cc TRUE
3. Examples
A simple example of t test:
- start R and type:
x=c(5.6,7.9,8.9,19.5,20.5,39.5)
y=c(6.5,8.3,9.1,17.9,29.4,22.8)
write.table(x, file = "foo1")
write.table(y, file = "foo2")
a<-read.table("foo1") # read the file
b<-read.table("foo2") # read the file
t.test(a,b,alternative=c("less") )
t.test(a,b,altrenative=c("less"),paired=TRUE) # paired t test
You can also write these into a file, script.R, then run
R CMD BATCH script.R
More R Examples:
4. More Readings and Practices
Basic:
- << Bioinformatics Data Skills >>
- A Rapid Introduction to the R Language
- Quick R 可以从如下章节开始 :
- Learning R
- R Interface
- Data Input
- Statistics
Advanced:
- Advanced R Tutorial
- << Bioinformatics Data Skills >>
- Working with Range Data
- Quick R