Contents

1. 1 Introduction

2. 2 R Basics

3. 3 Code Editors for R

4. 4 Integrating R with Vim and Tmux

5. 5 Finding Help

6. 6 Control Structures

1. 6.1 Conditional Executions

1. 6.1.1 Comparison Operators

2. 6.1.2 Logical Operators

3. 6.1.3 If Statements

4. 6.1.4 Ifelse Statements

2. 6.2 Loops

1. 6.2.1 For Loop

2. 6.2.2 While Loop

3. 6.2.3 Apply Loop Family

1. 6.2.3.1 For Two-Dimensional Data Sets: apply

2. 6.2.3.2 For Ragged Arrays: tapply

3. 6.2.3.3 For Vectors and Lists: lapply and sapply

4. 6.2.4 Other Loops

5. 6.2.5 Improving Speed Performance of Loops

7. 7 Functions

8. 8 Useful Utilities

1. 8.1 Debugging Utilities

 2. 8.2 Regular Expressions

3. 8.3 Interpreting Character String as Expression

4. 8.4 Time, Date and Sleep

5. 8.5 Calling External Software with System Command

6. 8.6 Miscellaneous Utilities

9. 9 Running R Programs

10. 10 Object-Oriented Programming (OOP)

1. 10.1 Define S4 Classes

2. 10.2 Assign Generics and Methods

11. 11 Building R Packages

12. 12 Reproducible Research by Integrating R with Latex or Markdown

13. 13 R Programming Exercises

1. 13.1 Exercise Slides

2. 13.2 Sample Scripts

1. 13.2.1 Batch Operations on Many Files

2. 13.2.2 Large-scale Array Analysis

3. 13.2.3 Graphical Procedures: Feature Map Example

4. 13.2.4 Sequence Analysis Utilities

5. 13.2.5 Pattern Matching and Positional Parsing of Sequences

6. 13.2.6 Identify Over-Represented Strings in Sequence Sets

7. 13.2.7 Translate DNA into Protein

8. 13.2.8 Subsetting of Structure Definition Files (SDF)

9. 13.2.9 Managing Latex BibTeX Databases

 10. 13.2.10 Loan Payments and Amortization Tables

11. 13.2.11 Course Assignment: GC Content, Reverse & Complement

14. 14 Translation of this Page

Introduction

[ Slides ] [ R Code ]

General Overview
One of the main attractions of using the R (http://cran.at.r-project.org) environment is the ease with
which users can write their own programs and custom functions. The R programming syntax is
extremely easy to learn, even for users with no previous programming experience. Once the
basic R programming control structures are understood, users can use the R language as a
powerful environment to perform complex custom analyses of almost any type of data.

Format of this Manual

In this manual all commands are given in code boxes, where the R code is printed in black, the
comment text in blue and the output generated by R in green. All comments/explanations start
with the standard comment sign '#' to prevent them from being interpreted by R as commands.
This way the content in the code boxes can be pasted with their comment text into the R console
to evaluate their utility. Occasionally, several commands are printed on one line and separated by
a semicolon ';'. Commands starting with a '$' sign need to be executed from a Unix or Linux
shell. Windows users can simply ignore them.

R Basics
The R & BioConductor manual provides a general introduction to the usage of the R
environment and its basic command syntax.

Code Editors for R

Several excellent code editors are available that provide functionalities like R syntax
highlighting, auto code indenting and utilities to send code/functions to the R console.
 Basic code editors provided by Rguis
 RStudio: GUI-based IDE for R
 Vim-R-Tmux: R working environment based on vim and tmux
 Emacs (ESS add-on package)
 gedit and Rgedit
 RKWard
 Eclipse
 Tinn-R
 Notepad++ (NppToR)

Programming in R using Vim or Emacs

Programming in R using RStudio
Integrating R with Vim and Tmux
Users interested in integrating R with vim and tmux may want to consult the Vim-R-Tmux
configuration page.

Finding Help
Reference list on R programming (selection)
 R Programming for Bioinformatics, by Robert Gentleman
 Advanced R, by Hadley Wickham

 S Programming, by W. N. Venables and B. D. Ripley

 Programming with Data, by John M. Chambers
 R Help & R Coding Conventions, Henrik Bengtsson, Lund University
 Programming in R (Vincent Zoonekynd)
 Peter's R Programming Pages, University of Warwick
 Rtips, Paul Johnsson, University of Kansas
 R for Programmers, Norm Matloff, UC Davis
 High-Performance R, Dirk Eddelbuettel tutorial presented at useR-2008
 C/C++ level programming for R, Gopi Goswami

Control Structures
Conditional Executions
Comparison Operators
 equal: ==
 not equal: !=

 greater/less than: > <

  greater/less than or equal: >= <=

Logical Operators
 and: &
 or: |

 not: !

If Statements
If statements operate on length-one logical vectors.

Syntax
if(cond1=true) { cmd1 } else { cmd2 }

Example
if(1==0) {
print(1)
} else {
print(2)
}
[1] 2
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Avoid inserting newlines between '} else'.

Ifelse Statements
Ifelse statements operate on vectors of variable length.

Syntax
ifelse(test, true_value, false_value)

Example
x <- 1:10 # Creates sample data
ifelse(x<5 | x>8, x, 0)
[1] 1 2 3 4 0 0 0 0 9 10
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Loops
The most commonly used loop structures in R are for, while and apply loops. Less common
are repeat loops. The break function is used to break out of loops, and next halts the
processing of the current iteration and advances the looping index.

For Loop
For loops are controlled by a looping vector. In every iteration of the loop one value in the
looping vector is assigned to a variable that can be used in the statements of the body of the loop.
Usually, the number of loop iterations is defined by the number of values stored in the looping
vector and they are processed in the same order as they are stored in the looping vector.

Syntax
for(variable in sequence) {
statements
}

Example
mydf <- iris
myve <- NULL # Creates empty storage container
for(i in seq(along=mydf[,1])) {
myve <- c(myve, mean(as.numeric(mydf[i, 1:3]))) # Note: inject approach is
much faster than append with 'c'. See below for details.
}
myve
[1] 3.333333 3.100000 3.066667 3.066667 3.333333 3.666667 3.133333 3.300000
[9] 2.900000 3.166667 3.533333 3.266667 3.066667 2.800000 3.666667 3.866667
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Example: condition*
x <- 1:10
z <- NULL
for(i in seq(along=x)) {
if(x[i] < 5) {
z <- c(z, x[i] - 1)
} else {
z <- c(z, x[i] / x[i])
}
}
z
[1] 0 1 2 3 1 1 1 1 1 1
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Example: stop on condition and print error message

x <- 1:10
z <- NULL
for(i in seq(along=x)) {
if (x[i]<5) {
z <- c(z,x[i]-1)
} else {
stop("values need to be <5")
}
}
Error: values need to be <5
z
[1] 0 1 2 3
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While Loop
Similar to for loop, but the iterations are controlled by a conditional statement.

Syntax
while(condition) statements

Example
z <- 0
while(z < 5) {
z <- z + 2
print(z)
}
[1] 2
[1] 4
[1] 6
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Apply Loop Family

For Two-Dimensional Data Sets: apply

Syntax
apply(X, MARGIN, FUN, ARGs)

X: array, matrix or data.frame; MARGIN: 1 for rows, 2 for columns, c(1,2) for both; FUN:
one or more functions; ARGs: possible arguments for function

Example
## Example for applying predefined mean function
apply(iris[,1:3], 1, mean)
[1] 3.333333 3.100000 3.066667 3.066667 3.333333 3.666667 3.133333 3.300000
...

## With custom function

x <- 1:10
test <- function(x) { # Defines some custom function
if(x < 5) {
x-1
} else {
x / x
}
}
apply(as.matrix(x), 1, test) # Returns same result as previous for loop*
[1] 0 1 2 3 1 1 1 1 1 1

## Same as above but with a single line of code

apply(as.matrix(x), 1, function(x) { if (x<5) { x-1 } else { x/x } })
[1] 0 1 2 3 1 1 1 1 1 1
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For Ragged Arrays: tapply

Applies a function to array categories of variable lengths (ragged array). Grouping is defined by
factor.

Syntax
tapply(vector, factor, FUN)

Example

## Computes mean values of vector agregates defined by factor

tapply(as.vector(iris[,4]), factor(iris[,5]), mean)
setosa versicolor virginica
0.246 1.326 2.026

## The aggregate function provides related utilities

aggregate(iris[,1:4], list(iris$Species), mean)
Group.1 Sepal.Length Sepal.Width Petal.Length Petal.Width
1 setosa 5.006 3.428 1.462 0.246
2 versicolor 5.936 2.770 4.260 1.326
3 virginica 6.588 2.974 5.552 2.026
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For Vectors and Lists: lapply and sapply

Both apply a function to vector or list objects. The function lapply returns a list,
while sapply attempts to return the simplest data object, such as vector or matrix instead
of list.

Syntax

lapply(X, FUN)
sapply(X, FUN)

Example
## Creates a sample list
mylist <- as.list(iris[1:3,1:3])
mylist
$Sepal.Length
[1] 5.1 4.9 4.7

$Sepal.Width
[1] 3.5 3.0 3.2

$Petal.Length
[1] 1.4 1.4 1.3

## Compute sum of each list component and return result as list

lapply(mylist, sum)
$Sepal.Length
[1] 14.7

$Sepal.Width
[1] 9.7

$Petal.Length
[1] 4.1

## Compute sum of each list component and return result as vector

sapply(mylist, sum)
Sepal.Length Sepal.Width Petal.Length
14.7 9.7 4.1
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Other Loops
Repeat Loop

Syntax

repeat statements

Loop is repeated until a break is specified. This means there needs to be a second statement to
test whether or not to break from the loop.

Example
z <- 0
repeat {
z <- z + 1
print(z)
if(z > 100) break()
}
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Improving Speed Performance of Loops

Looping over very large data sets can become slow in R. However, this limitation can be
overcome by eliminating certain operations in loops or avoiding loops over the data intensive
dimension in an object altogether. The latter can be achieved by performing mainly vector-to-
vecor or matrix-to-matrix computations which run often over 100 times faster than the
corresponding for() or apply() loops in R. For this purpose, one can make use of the existing
speed-optimized R functions (e.g.: rowSums, rowMeans, table, tabulate) or one can design
custom functions that avoid expensive R loops by using vector- or matrix-based approaches.
Alternatively, one can write programs that will perform all time consuming computations on the
C-level.

(1) Speed comparison of for loops with an append versus an inject step:
myMA <- matrix(rnorm(1000000), 100000, 10, dimnames=list(1:100000, paste("C",
1:10, sep="")))
results <- NULL
system.time(for(i in seq(along=myMA[,1])) results <- c(results,
mean(myMA[i,])))
user system elapsed
39.156 6.369 45.559

results <- numeric(length(myMA[,1]))

system.time(for(i in seq(along=myMA[,1])) results[i] <- mean(myMA[i,]))
user system elapsed
1.550 0.005 1.556
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The inject approach is 20-50 times faster than the append version.

(2) Speed comparison of apply loop versus rowMeans for computing the mean for each row
in a large matrix:
system.time(myMAmean <- apply(myMA, 1, mean))
user system elapsed
1.452 0.005 1.456

system.time(myMAmean <- rowMeans(myMA))

user system elapsed
0.005 0.001 0.006
 Table of Contents
The rowMeans approach is over 200 times faster than the apply loop.

(3) Speed comparison of apply loop versus vectorized approach for computing the standard
deviation of each row:
system.time(myMAsd <- apply(myMA, 1, sd))
user system elapsed
3.707 0.014 3.721
myMAsd[1:4]
1 2 3 4
0.8505795 1.3419460 1.3768646 1.3005428

system.time(myMAsd <- sqrt((rowSums((myMA-rowMeans(myMA))^2)) /

(length(myMA[1,])-1)))
user system elapsed
0.020 0.009 0.028

myMAsd[1:4]
1 2 3 4
0.8505795 1.3419460 1.3768646 1.3005428
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The vector-based approach in the last step is over 200 times faster than the apply loop.

(4) Example for computing the mean for any custom selection of columns without compromising
the speed performance:
## In the following the colums are named according to their selection in
myList
myList <- tapply(colnames(myMA), c(1,1,1,2,2,2,3,3,4,4), list)
myMAmean <- sapply(myList, function(x) rowMeans(myMA[,x]))
colnames(myMAmean) <- sapply(myList, paste, collapse="_")
myMAmean[1:4,]
C1_C2_C3 C4_C5_C6 C7_C8 C9_C10
1 0.0676799 -0.2860392 0.09651984 -0.7898946
2 -0.6120203 -0.7185961 0.91621371 1.1778427
3 0.2960446 -0.2454476 -1.18768621 0.9019590
4 0.9733695 -0.6242547 0.95078869 -0.7245792

## Alternative to achieve the same result with similar performance, but in a

much less elegant way
myselect <- c(1,1,1,2,2,2,3,3,4,4) # The colums are named according to the
selection stored in myselect
myList <- tapply(seq(along=myMA[1,]), myselect, function(x) paste("myMA[ ,",
x, "]", sep=""))
myList <- sapply(myList, function(x) paste("(", paste(x, collapse=" + "),")/",
length(x)))
myMAmean <- sapply(myList, function(x) eval(parse(text=x)))
colnames(myMAmean) <- tapply(colnames(myMA), myselect, paste, collapse="_")
myMAmean[1:4,]
C1_C2_C3 C4_C5_C6 C7_C8 C9_C10
1 0.0676799 -0.2860392 0.09651984 -0.7898946
2 -0.6120203 -0.7185961 0.91621371 1.1778427
3 0.2960446 -0.2454476 -1.18768621 0.9019590
4 0.9733695 -0.6242547 0.95078869 -0.7245792
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Functions
A very useful feature of the R environment is the possibility to expand existing functions and to
easily write custom functions. In fact, most of the R software can be viewed as a series of R
functions.

Syntax to define functions

myfct <- function(arg1, arg2, ...) {
function_body
}
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The value returned by a function is the value of the function body, which is usually an
unassigned final expression, e.g.: return()

Syntax to call functions

myfct(arg1=..., arg2=...)
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Syntax Rules for Functions

General
Functions are defined by (1) assignment with the keyword function, (2) the declaration of
arguments/variables (arg1, arg2, ...) and (3) the definition of operations
(function_body) that perform computations on the provided arguments. A function name
needs to be assigned to call the function (see below).

Naming
Function names can be almost anything. However, the usage of names of existing functions
should be avoided.

Arguments
It is often useful to provide default values for arguments (e.g.:arg1=1:10). This way they don't
need to be provided in a function call. The argument list can also be left empty (myfct <-
function() { fct_body }) when a function is expected to return always the same
value(s). The argument '...' can be used to allow one function to pass on argument settings to
another.

Function body
The actual expressions (commands/operations) are defined in the function body which should be
enclosed by braces. The individual commands are separated by semicolons or new lines
(preferred).

Calling functions
Functions are called by their name followed by parentheses containing possible argument names.
Empty parenthesis after the function name will result in an error message when a function
requires certain arguments to be provided by the user. The function name alone will print the
definition of a function.

Scope
Variables created inside a function exist only for the life time of a function. Thus, they are not
accessible outside of the function. To force variables in functions to exist globally, one can use
this special assignment operator: '<<-'. If a global variable is used in a function, then the global
variable will be masked only within the function.

Example: Function basics

myfct <- function(x1, x2=5) {
z1 <- x1/x1
z2 <- x2*x2
myvec <- c(z1, z2)
return(myvec)
}
myfct # prints definition of function
myfct(x1=2, x2=5) # applies function to values 2 and 5
[1] 1 25

myfct(2, 5) # the argument names are not necessary, but then the order of the
specified values becomes important
myfct(x1=2) # does the same as before, but the default value '5' is used in
this case
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Example: Function with optional arguments

myfct2 <- function(x1=5, opt_arg) {
if(missing(opt_arg)) { # 'missing()' is used to test whether a value
was specified as an argument
z1 <- 1:10
} else {
z1 <- opt_arg
}
cat("my function returns:", "\n")
return(z1/x1)
}
myfct2(x1=5) # performs calculation on default vector (z1) that is defined in
the function body
my function returns:
[1] 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0
myfct2(x1=5, opt_arg=30:20) # a custom vector is used instead when the
optional argument (opt_arg) is specified
my function returns:
[1] 6.0 5.8 5.6 5.4 5.2 5.0 4.8 4.6 4.4 4.2 4.0
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Control utilities for functions: return, warning and stop

Return
The evaluation flow of a function may be terminated at any stage with the return function.
This is often used in combination with conditional evaluations.

Stop
To stop the action of a function and print an error message, one can use the stop function.

Warning
To print a warning message in unexpected situations without aborting the evaluation flow of a
function, one can use the function warning("...").

myfct <- function(x1) {

if (x1>=0) print(x1) else stop("This function did not finish, because
x1 < 0")
warning("Value needs to be > 0")
}
myfct(x1=2)
[1] 2
Warning message:
In myfct(x1 = 2) : Value needs to be > 0

myfct(x1=-2)
Error in myfct(x1 = -2) : This function did not finish, because x1 < 0
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Useful Utilities
Debugging Utilities
Several debugging utilities are available for R. The most important utilities
are: traceback(), browser(), options(error=recover), options(error=NUL
L) and debug(). The Debugging in Rpage provides an overview of the available resources.

Regular Expressions
R's regular expression utilities work similar as in other languages. To learn how to use them in R,
one can consult the main help page on this topic with ?regexp. The following gives a few
basic examples.
The grep function can be used for finding patterns in strings, here letter A in
vector month.name.
month.name[grep("A", month.name)]
[1] "April" "August"
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Example for using regular expressions to substitute a pattern by another one using
the sub/gsub function with a back reference. Remember: single escapes '\' need to be double
escaped '\\' in R.
gsub("(i.*a)", "xxx_\\1", "virginica", perl = TRUE)
[1] "vxxx_irginica"
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Example for split and paste functions

x <- gsub("(a)", "\\1_", month.name[1], perl=TRUE) # performs substitution
with back reference which inserts in this example a '_' character
x
[1] "Ja_nua_ry"

strsplit(x, "_") # splits string on inserted character from above

[[1]]
[1] "Ja" "nua" "ry"

paste(rev(unlist(strsplit(x, NULL))), collapse="") # reverses character string

by splitting first all characters into vector fields and then collapsing them
with paste
[1] "yr_aun_aJ"
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Example for importing specific lines in a file with a regular expression. The following example
demonstrates the retrieval of specific lines from an external file with a regular expression. First,
an external file is created with the cat function, all lines of this file are imported into a vector
with readLines, the specific elements (lines) are then retieved with the grep function, and
the resulting lines are split into vector fields with strsplit.
cat(month.name, file="zzz.txt", sep="\n")
x <- readLines("zzz.txt")
x <- x[c(grep("^J", as.character(x), perl = TRUE))]
t(as.data.frame(strsplit(x, "u")))
[,1] [,2]
c..Jan....ary.. "Jan" "ary"
c..J....ne.. "J" "ne"
c..J....ly.. "J" "ly"
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Interpreting Character String as Expression
Example

mylist <- ls() # generates vector of object names in session

mylist[1] # prints name of 1st entry in vector but does not execute it as
expression that returns values of 10th object
get(mylist[1]) # uses 1st entry name in vector and executes it as expression
eval(parse(text=mylist[1])) # alternative approach to obtain similar result
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Time, Date and Sleep

Example

system.time(ls()) # returns CPU (and other) times that an expression used,

here ls()
user system elapsed
0 0 0

date() # returns the current system date and time

[1] "Wed Dec 11 15:31:17 2012"

Sys.sleep(1) # pause execution of R expressions for a given number of seconds

(e.g. in loop)
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Calling External Software with System Command

The system command allows to call any command-line software from within R on Linux, UNIX
and OSX systems.
system("...") # provide under '...' command to run external software e.g.
Perl, Python, C++ programs
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Related utilities on Windows operating systems

x <- shell("dir", intern=T) # reads current working directory and assigns to
file
shell.exec("C:/Documents and Settings/Administrator/Desktop/my_file.txt") #
opens file with associated program
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Miscellaneous Utilities
(1) Batch import and export of many files.
In the following example all file names ending with *.txt in the current directory are first
assigned to a list (the '$' sign is used to anchor the match to the end of a string). Second, the files
are imported one-by-one using a for loop where the original names are assigned to the generated
data frames with the assign function. Consult help with ?read.table to understand
arguments row.names=1 and comment.char = "A". Third, the data frames are exported
using their names for file naming and appending the extension *.out.
files <- list.files(pattern=".txt$")
for(i in files) {
x <- read.table(i, header=TRUE, comment.char = "A", sep="\t")
assign(i, x)
print(i)
write.table(x, paste(i, c(".out"), sep=""), quote=FALSE, sep="\t",
col.names = NA)
}
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(2) Running Web Applications (basics on designing web client/crawling/scraping scripts in R)

Example for obtaining MW values for peptide sequences from the EXPASY's pI/MW Tool web
page.
myentries <- c("MKWVTFISLLFLFSSAYS", "MWVTFISLL",
"MFISLLFLFSSAYS")

myresult <-
NULL

for(i in myentries)
{

myurl <- paste("http://ca.expasy.org/cgi-bin/pi_tool?protein=", i,

"&resolution=monoisotopic", sep="")
x <-
url(myurl)

res <-
readLines(x)

close(x)

mylines <- res[grep("Theoretical pI/Mw:",

res)]
 myresult <- c(myresult, as.numeric(gsub(".*/ ", "",
mylines)))

print(myresult)

Sys.sleep(1) # halts process for one sec to give web service a

break

final <- data.frame(Pep=myentries,

MW=myresult)

cat("\n The MW values for my peptides are:\

n")

final
Pep MW
1 MKWVTFISLLFLFSSAYS 2139.11
2 MWVTFISLL 1108.60
3 MFISLLFLFSSAYS 1624.82
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Running R Programs
(1) Executing an R script from the R console
source("my_script.R")
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(2.1) Syntax for running R programs from the command-line. Requires in first line
of my_script.R the following statement: #!/usr/bin/env Rscript
$ Rscript my_script.R # or just ./myscript.R after making file executable with
'chmod +x my_script.R'

All commands starting with a '$' sign need to be executed from a Unix or Linux shell.

(2.2) Alternatively, one can use the following syntax to run R programs in BATCH mode from
the command-line.
$ R CMD BATCH [options] my_script.R [outfile]

The output file lists the commands from the script file and their outputs. If no outfile is specified,
the name used is that of infile and .Rout is appended to outfile. To stop all the usual R
command line information from being written to the outfile, add this as first line
to my_script.R file: options(echo=FALSE). If the command is run like this R CMD
BATCH --no-save my_script.R, then nothing will be saved in the .Rdata file which
can get often very large. More on this can be found on the help pages: $ R CMD BATCH --
help or ?BATCH.
(2.3) Another alternative for running R programs as silently as possible.
$ R --slave < my_infile > my_outfile

Argument --slave makes R run as 'quietly' as possible.

(3) Passing Command-Line Arguments to R Programs
Create an R script, here named test.R, like this one:

######################
myarg <- commandArgs()
print(iris[1:myarg[6], ])
######################

Then run it from the command-line like this:

$ Rscript test.R 10
In the given example the number 10 is passed on from the command-line as an argument to the R
script which is used to return to STDOUT the first 10 rows of the iris sample data. If several
arguments are provided, they will be interpreted as one string that needs to be split it in R with
the strsplit function.

(4) Submitting R script to a Linux cluster via Torque

Create the following shell script my_script.sh
#################################
#!/bin/bash
cd $PBS_O_WORKDIR
R CMD BATCH --no-save my_script.R
#################################
This script doesn't need to have executable permissions. Use the following qsub command to
send this shell script to the Linux cluster from the directory where the R
script my_script.R is located. To utilize several CPUs on the Linux cluster, one can divide
the input data into several smaller subsets and execute for each subset a separate process from a
dedicated directory.
$ qsub my_script.sh
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Here is a short R script that generates the required files and directories automatically and submits
the jobs to the nodes: submit2cluster.R. For more details, see also this 'Tutorial on Parallel
Programming in R' by Hanna Sevcikova

(5) Submitting jobs to Torque or any other queuing/scheduling system via

the BatchJobs package. This package provides one of the most advanced resources for
submitting jobs to queuing systems from within R. A related package is BiocParallel from
Bioconductor which extends many functionalities of BatchJobs to genome data analysis.
Useful documentation for BatchJobs: Technical Report, GitHub page, Slide Show, Config
samples.
library(BatchJobs)
loadConfig(conffile = ".BatchJobs.R")
## Loads configuration file. Here .BatchJobs.R containing just this
line:
## cluster.functions <- makeClusterFunctionsTorque("torque.tmpl")
## The template file torque.tmpl is expected to be in the current
working
## director. It can be downloaded from here:
## https://github.com/tudo-r/BatchJobs/blob/master/examples/cfTorque/
simple.tmpl

getConfig() # Returns BatchJobs configuration settings

reg <- makeRegistry(id="BatchJobTest", work.dir="results")
## Constructs a registry object. Output files from R will be stored
under directory "results",
## while the standard objects from BatchJobs will be stored in the
directory "BatchJobTest-files".
print(reg)

## Some test function

f <- function(x) {
system("ls -al >> test.txt")
x
}

## Adds jobs to registry object (here reg)

ids <- batchMap(reg, fun=f, 1:10)
print(ids)
showStatus(reg)

## Submit jobs or chunks of jobs to batch system via cluster function

done <- submitJobs(reg, resources=list(walltime=3600, nodes="1:ppn=4",
memory="4gb"))

## Load results from BatchJobTest-files/jobs/01/1-result.RData

loadResult(reg, 1)
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Object-Oriented Programming (OOP)

R supports two systems for object-oriented programming (OOP). An older S3 system and a more
recently introduced S4 system. The latter is more formal, supports multiple inheritance, multiple
dispatch and introspection. Many of these features are not available in the older S3 system. In
general, the OOP approach taken by R is to separate the class specifications from the
specifications of generic functions (function-centric system). The following introduction is
restricted to the S4 system since it is nowadays the preferred OOP method for R. More
information about OOP in R can be found in the following introductions: Vincent Zoonekynd's
introduction to S3 Classes, S4 Classes in 15 pages, Christophe Genolini's S4 Intro, The R.oo
package, BioC Course: Advanced R for Bioinformatics, Programming with R by John
Chambersand R Programming for Bioinformatics by Robert Gentleman.

Define S4 Classes
(A) Define S4 Classes with setClass() and new()
y <- matrix(1:50, 10, 5) # Sample data set
setClass(Class="myclass",
representation=representation(a="ANY"),
prototype=prototype(a=y[1:2,]), # Defines default value (optional)
validity=function(object) { # Can be defined in a separate step using
setValidity
if(class(object@a)!="matrix") {
return(paste("expected matrix, but obtained", class(object@a)))
} else {
return(TRUE)
}
}
)
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The setClass function defines classes. Its most important arguments are
 Class: the name of the class
 representation: the slots that the new class should have and/or other classes that
this class extends.
 prototype: an object providing default data for the slots.

 contains: the classes that this class extends.

 validity, access, version: control arguments included for compatibility with S-

Plus.
 where: the environment to use to store or remove the definition as meta data.

(B) The function new creates an instance of a class (here myclass)

myobj <- new("myclass", a=y)
myobj
An object of class "myclass"
Slot "a":
[,1] [,2] [,3] [,4] [,5]
[1,] 1 11 21 31 41
[2,] 2 12 22 32 42
...

new("myclass", a=iris) # Returns an error message due to wrong input type

(iris is data frame)
Error in validObject(.Object) :
invalid class “myclass” object: expected matrix, but obtained data.frame
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Its arguments are:
 Class: the name of the class
 ...: Data to include in the new object with arguments according to slots in class
definition.

(C) A more generic way of creating class instances is to define an initialization method (details
below)
setMethod("initialize", "myclass", function(.Object, a) {
.Object@a <- a/a
.Object
})
new("myclass", a = y)
[1] "initialize"
new("myclass", a = y)> new("myclass", a = y)
An object of class "myclass"
Slot "a":
[,1] [,2] [,3] [,4] [,5]
[1,] 1 1 1 1 1
[2,] 1 1 1 1 1
...
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(D) Usage and helper functions

myobj@a # The '@' extracts the contents of a slot. Usage should be limited to
internal functions!
initialize(.Object=myobj, a=as.matrix(cars[1:3,])) # Creates a new S4 object
from an old one.
# removeClass("myclass") # Removes object from current session; does not apply
to associated methods.
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(E) Inheritance: allows to define new classes that inherit all properties (e.g. data slots, methods)
from their existing parent classes
setClass("myclass1", representation(a = "character", b = "character"))
setClass("myclass2", representation(c = "numeric", d = "numeric"))
setClass("myclass3", contains=c("myclass1", "myclass2"))
new("myclass3", a=letters[1:4], b=letters[1:4], c=1:4, d=4:1)
An object of class "myclass3"
Slot "a":
[1] "a" "b" "c" "d"

Slot "b":
[1] "a" "b" "c" "d"

Slot "c":
[1] 1 2 3 4

Slot "d":
[1] 4 3 2 1
getClass("myclass1")
Class "myclass1" [in ".GlobalEnv"]

Slots:

Name: a b
Class: character character

Known Subclasses: "myclass3"

getClass("myclass2")
Class "myclass2" [in ".GlobalEnv"]

Slots:

Name: c d
Class: numeric numeric

Known Subclasses: "myclass3"

getClass("myclass3")
Class "myclass3" [in ".GlobalEnv"]

Slots:

Name: a b c d
Class: character character numeric numeric

Extends: "myclass1", "myclass2"

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The argument contains allows to extend existing classes; this propagates all slots of parent
classes.

(F) Coerce objects to another class

setAs(from="myclass", to="character", def=function(from)
as.character(as.matrix(from@a)))
as(myobj, "character")
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15"
...
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(G) Virtual classes are constructs for which no instances will be or can be created. They are used
to link together classes which may have distinct representations (e.g. cannot inherit from each
other) but for which one wants to provide similar functionality. Often it is desired to create a
virtual class and to then have several other classes extend it. Virtual classes can be defined by
leaving out the representation argument or including the class VIRTUAL:
setClass("myVclass")
setClass("myVclass", representation(a = "character", "VIRTUAL"))
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(H) Functions to introspect classes
 getClass("myclass")
 getSlots("myclass")
 slotNames("myclass")
 extends("myclass2")

Assign Generics and Methods

Assign generics and methods with setGeneric() and setMethod()
(A) Accessor function (to avoid usage of '@')
setGeneric(name="acc", def=function(x) standardGeneric("acc"))
setMethod(f="acc", signature="myclass", definition=function(x) {
return(x@a)
})
acc(myobj)
[,1] [,2] [,3] [,4] [,5]
[1,] 1 11 21 31 41
[2,] 2 12 22 32 42
...
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(B.1) Replacement method using custom accessor function (acc <-)

setGeneric(name="acc<-", def=function(x, value) standardGeneric("acc<-"))
setReplaceMethod(f="acc", signature="myclass", definition=function(x, value) {
x@a <- value
return(x)
})
## After this the following replace operations with 'acc' work on new object
class
acc(myobj)[1,1] <- 999 # Replaces first value
colnames(acc(myobj)) <- letters[1:5] # Assigns new column names
rownames(acc(myobj)) <- letters[1:10] # Assigns new row names
myobj
An object of class "myclass"
Slot "a":
a b c d e
a 999 11 21 31 41
b 2 12 22 32 42
...
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(B.2) Replacement method using "[" operator ([<-)

setReplaceMethod(f="[", signature="myclass", definition=function(x, i, j,
value) {
 x@a[i,j] <- value
return(x)
})
myobj[1,2] <- 999
myobj
An object of class "myclass"
Slot "a":
a b c d e
a 999 999 21 31 41
b 2 12 22 32 42
...
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(C) Define behavior of "[" subsetting operator (no generic required!)

setMethod(f="[", signature="myclass",
definition=function(x, i, j, ..., drop) {
x@a <- x@a[i,j]
return(x)
})
myobj[1:2,] # Standard subsetting works now on new class
An object of class "myclass"
Slot "a":
a b c d e
a 999 999 21 31 41
b 2 12 22 32 42
...
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(D) Define print behavior

setMethod(f= show", signature="myclass", definition=function(object) {
cat("An instance of ", "\"", class(object), "\"", " with ",
length(acc(object)[,1]), " elements", "\n", sep="")
if(length(acc(object)[,1])>=5) {
print(as.data.frame(rbind(acc(object)[1:2,], ...=rep("...",
length(acc(object)[1,])),
acc(object)[(length(acc(object)[,1])-1):length(acc(object)[,1]),])))
} else {
print(acc(object))
}})
myobj # Prints object with custom method
An instance of "myclass" with 10 elements
a b c d e
a 999 999 21 31 41
b 2 12 22 32 42
... ... ... ... ... ...
i 9 19 29 39 49
j 10 20 30 40 50
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(E) Define a data specific function (here randomize row order)

setGeneric(name="randomize", def=function(x) standardGeneric("randomize"))
setMethod(f="randomize", signature="myclass", definition=function(x) {
acc(x)[sample(1:length(acc(x)[,1]), length(acc(x)[,1])), ]
})
randomize(myobj)
a b c d e
j 10 20 30 40 50
b 2 12 22 32 42
...
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(F) Define a graphical plotting function and allow user to access it with generic plot function
setMethod(f="plot", signature="myclass", definition=function(x, ...) {
barplot(as.matrix(acc(x)), ...)
})
plot(myobj)
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(G) Functions to inspect methods

 showMethods(class="myclass")
 findMethods("randomize")
 getMethod("randomize", signature="myclass")
 existsMethod("randomize", signature="myclass")

Building R Packages
To get familiar with the structure, building and submission process of R packages, users should
carefully read the documentation on this topic available on these sites:
 Writing R Extensions, R web site
 R Packages, by Hadley Wickham
 R Package Primer, by Karl Broman
 Package Guidelines, Bioconductor
 Advanced R Programming Class, Bioconductor

Short Overview of Package Building Process

(A) Automatic package building with the package.skeleton function:

package.skeleton(name="mypackage", code_files=c("script1.R", "script2.R"))
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Note: this is an optional but very convenient function to get started with a new package. The
given example will create a directory named mypackage containing the skeleton of the
package for all functions, methods and classes defined in the R script(s) passed on to
the code_files argument. The basic structure of the package directory is described here. The
package directory will also contain a file named 'Read-and-delete-me' with the following
instructions for completing the package:
 Edit the help file skeletons in man, possibly combining help files for multiple functions.
 Edit the exports in NAMESPACE, and add necessary imports.

 Put any C/C++/Fortran code in src.

 If you have compiled code, add a useDynLib() directive to NAMESPACE.

 Run R CMD build to build the package tarball.

 Run R CMD check to check the package tarball.

 Read Writing R Extensions for more information.

(B) Once a package skeleton is available one can build the package from the command-line
(Linux/OS X):
$ R CMD build mypackage
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This will create a tarball of the package with its version number encoded in the file name,
e.g.: mypackage_1.0.tar.gz.
Subsequently, the package tarball needs to be checked for errors with:
$ R CMD check mypackage_1.0.tar.gz
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All issues in a package's source code and documentation should be addressed until R CMD
check returns no error or warning messages anymore.

(C) Install package from source:

Linux:
install.packages("mypackage_1.0.tar.gz", repos=NULL)
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OS X:
install.packages("mypackage_1.0.tar.gz", repos=NULL, type="source")
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Windows requires a zip archive for installing R packages, which can be most conveniently
created from the command-line (Linux/OS X) by installing the package in a local directory (here
tempdir) and then creating a zip archive from the installed package directory:
$ mkdir tempdir
$ R CMD INSTALL -l tempdir mypackage_1.0.tar.gz
$ cd tempdir
$ zip -r mypackage mypackage

## The resulting mypackage.zip archive can be installed under Windows like

this:
install.packages("mypackage.zip", repos=NULL)
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This procedure only works for packages which do not rely on compiled code (C/C++).
Instructions to fully build an R package under Windows can be found here and here.

(D) Maintain/expand an existing package:

 Add new functions, methods and classes to the script files in the ./R directory in your
package
 Add their names to the NAMESPACE file of the package

 Additional *.Rd help templates can be generated with the prompt*() functions like
this:

source("myscript.R") # imports functions, methods and classes from myscript.R

prompt(myfct) # writes help file myfct.Rd
promptClass("myclass") # writes file myclass-class.Rd
promptMethods("mymeth") # writes help file mymeth.Rd
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 The resulting *.Rd help files can be edited in a text editor and properly rendered
and viewed from within R like this:

library(tools)
Rd2txt("./mypackage/man/myfct.Rd") # renders *.Rd files as they look in final
help pages
checkRd("./mypackage/man/myfct.Rd") # checks *.Rd help file for problems
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(E) Submit package to a public repository

The best way of sharing an R package with the community is to submit it to one of the main R
package repositories, such as CRAN or Bioconductor. The details about the submission process
are given on the corresponding repository submission pages:
 Submitting to Bioconductor (guidelines, submission, svn control, build/checks
release, build/checks devel)
 Submitting to CRAN

Reproducible Research by Integrating R with Latex or

Markdown
  See Sweave/Stangle sections of Slide Show for this manual
 Sweave Manual
 R Markdown
 knitr manual
 RStudio's Rpubs page

R Programming Exercises
Exercise Slides
[ Slides ] [ Exercises ] [ Additional Exercises ]

Download on of the above exercise files, then start editing this R source file with a programming
text editor, such as Vim, Emacs or one of the R GUI text editors. Here is the HTML version of
the code with syntax coloring.

Sample Scripts
Batch Operations on Many Files
## (1) Start R from an empty test directory
## (2) Create some files as sample data
for(i in month.name) {
mydf <- data.frame(Month=month.name, Rain=runif(12, min=10, max=100),
Evap=runif(12, min=1000, max=2000))
write.table(mydf, file=paste(i , ".infile", sep=""), quote=F,
row.names=F, sep="\t")
}

## (3) Import created files, perform calculations and export to renamed files
files <- list.files(pattern=".infile$")
for(i in seq(along=files)) { # start for loop with numeric or character
vector; numeric vector is often more flexible
x <- read.table(files[i], header=TRUE, row.names=1, comment.char =
"A", sep="\t")
x <- data.frame(x, sum=apply(x, 1, sum), mean=apply(x, 1, mean)) #
calculates sum and mean for each data frame
assign(files[i], x) # generates data frame object and names it after
content in variable 'i'
print(files[i], quote=F) # prints loop iteration to screen to check
its status
write.table(x, paste(files[i], c(".out"), sep=""), quote=FALSE, sep="\
t", col.names = NA)
}
## (4) Same as above, but file naming by index data frame. This way one can
organize file names by external table.
name_df <- data.frame(Old_name=sort(files), New_name=sort(month.abb))
for(i in seq(along=name_df[,1])) {
x <- read.table(as.vector(name_df[i,1]), header=TRUE, row.names=1,
comment.char = "A", sep="\t")
x <- data.frame(x, sum=apply(x, 1, sum), mean=apply(x, 1, mean))
assign(as.vector(name_df[i,2]), x) # generates data frame object and
names it after 'i' entry in column 2
print(as.vector(name_df[i,1]), quote=F)
write.table(x, paste(as.vector(name_df[i,2]), c(".out"), sep=""),
quote=FALSE, sep="\t", col.names = NA)
}

## (5) Append content of all input files to one file.

files <- list.files(pattern=".infile$")
all_files <- data.frame(files=NULL, Month=NULL, Gain=NULL , Loss=NULL,
sum=NULL, mean=NULL) # creates empty data frame container
for(i in seq(along=files)) {
x <- read.table(files[i], header=TRUE, row.names=1, comment.char =
"A", sep="\t")
x <- data.frame(x, sum=apply(x, 1, sum), mean=apply(x, 1, mean))
x <- data.frame(file=rep(files[i], length(x[,1])), x) # adds file
tracking column to x
all_files <- rbind(all_files, x) # appends data from all files to data
frame 'all_files'
write.table(all_files, file="all_files.xls", quote=FALSE, sep="\t",
col.names = NA)
}

## (6) Write the above code into a text file and execute it with the commands
'source' and 'BATCH'.
source("my_script.R") # execute from R console
$ R CMD BATCH my_script.R # execute from shell
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Large-scale Array Analysis

Sample script to perform large-scale expression array analysis with complex queries: lsArray.R.
To demo what the script does, run it like this:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
lsArray.R")
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Graphical Procedures: Feature Map Example

Script to plot feature maps of genes or chromosomes: featureMap.R. To demo what the script
does, run it like this:
source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
featureMap.txt")
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Sequence Analysis Utilities

Includes sequence batch import, sub-setting, pattern matching, AA Composition, NEEDLE, PHYLIP, etc.
The script 'sequenceAnalysis.R' demonstrates how R can be used as a powerful tool for managing and
analyzing large sets of biological sequences. This example also shows how easy it is to integrate R with
the EMBOSS project or other external programs. The script provides the following functionality:
 Batch sequence import into R data frame
 Motif searching with hit statistics

 Analysis of sequence composition

 All-against-all sequence comparisons

 Generation of phylogenetic trees

To demonstrate the utilities of the script, users can simply execute it from R with the following source
command:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
sequenceAnalysis.txt")
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Pattern Matching and Positional Parsing of Sequences

Functions for importing sequences into R, retrieving reverse and complement of nucleotide sequences,
pattern searching, positional parsing and exporting search results in HTML format: patternSearch.R. To
demo what the script does, run it like this:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
patternSearch.R")
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Identify Over-Represented Strings in Sequence Sets

Functions for finding over-represented words in sets of DNA, RNA or protein sequences: wordFinder.R.
To demo what the script does, run it like this:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
wordFinder.R")
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Translate DNA into Protein

Script 'translateDNA.R' for translating NT sequences into AA sequences (required codon table). To demo
what the script does, run it like this:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
translateDNA.R")
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Subsetting of Structure Definition Files (SDF)

Script for importing and subsetting SDF files: sdfSubset.R. To demo what the script does, run it like this:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
sdfSubset.R")
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Managing Latex BibTeX Databases

Script for importing BibTeX databases into R, retrieving the individual references with a full-text search
function and viewing the results in R or in HubMed: BibTex.R. To demo what the script does, run it like
this:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
BibTex.R")
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Loan Payments and Amortization Tables

This script calculates monthly and annual mortgage or loan payments, generates amortization tables and
plots the results: mortgage.R. To demo what the script does, run it like this:

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/
mortgage.R")
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Course Assignment: GC Content, Reverse & Complement

Apply the above information to write a function that calculates for a set of DNA sequences their
GC content and generates their reverse and complement. Here are some useful commands that
can be incorporated in this function:

## Generate an example data frame with ID numbers and DNA sequences

fx <- function(test) {
x <- as.integer(runif(20, min=1, max=5))
x[x==1] <- "A"; x[x==2] <- "T"; x[x==3] <- "G"; x[x==4] <- "C"
paste(x, sep = "", collapse ="")
}
z1 <- c()
for(i in 1:50) {
z1 <- c(fx(i), z1)
}
z1 <- data.frame(ID=seq(along=z1), Seq=z1)
z1

## Write each character of sequence into separate vector field and reverse its
order
my_split <- strsplit(as.character(z1[1,2]),"")
my_rev <- rev(my_split[[1]])
paste(my_rev, collapse="")

## Generate the sequence complement by replacing G|C|A|T by C|G|T|A

## Use 'apply' or 'for loop' to apply the above operations to all sequences in
sample data frame 'z1'
## Calculate in the same loop the GC content for each sequence using the
following command
table(my_split[[1]])/length(my_split[[1]])