#rgedit | Explore Tumblr Posts and Blogs

oditile · 7 years

Text

Programming in R

From: http://manuals.bioinformatics.ucr.edu/home/programming-in-r

Author:

Thomas Girke

,

UC Riverside

Contents

1 Introduction

2 R Basics

3 Code Editors for R

4 Integrating R with Vim and Tmux

5 Finding Help

6 Control Structures

7 Functions

8 Useful Utilities

9 Running R Programs

10 Object-Oriented Programming (OOP)

11 Building R Packages

12 Reproducible Research by Integrating R with Latex or Markdown

13 R Programming Exercises

14 Translation of this Page

6.1 Conditional Executions

6.2 Loops

6.1.1 Comparison Operators

6.1.2 Logical Operators

6.1.3 If Statements

6.1.4 Ifelse Statements

6.2.1 For Loop

6.2.2 While Loop

6.2.3 Apply Loop Family

6.2.4 Other Loops

6.2.5 Improving Speed Performance of Loops

6.2.3.1 For Two-Dimensional Data Sets: apply

6.2.3.2 For Ragged Arrays: tapply

6.2.3.3 For Vectors and Lists: lapply and sapply

8.1 Debugging Utilities

8.2 Regular Expressions

8.3 Interpreting Character String as Expression

8.4 Time, Date and Sleep

8.5 Calling External Software with System Command

8.6 Miscellaneous Utilities

10.1 Define S4 Classes

10.2 Assign Generics and Methods

13.1 Exercise Slides

13.2 Sample Scripts

13.2.1 Batch Operations on Many Files

13.2.2 Large-scale Array Analysis

13.2.3 Graphical Procedures: Feature Map Example

13.2.4 Sequence Analysis Utilities

13.2.5 Pattern Matching and Positional Parsing of Sequences

13.2.6 Identify Over-Represented Strings in Sequence Sets

13.2.7 Translate DNA into Protein

13.2.8 Subsetting of Structure Definition Files (SDF)

13.2.9 Managing Latex BibTeX Databases

13.2.10 Loan Payments and Amortization Tables

13.2.11 Course Assignment: GC Content, Reverse & Complement

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 StatementsIf 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

Table of Contents

Avoid inserting newlines between '} else'.

Ifelse StatementsIfelse 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

Table of Contents

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 LoopFor 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

Table of Contents

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

Table of Contents

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

Table of Contents

While LoopSimilar 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

Table of Contents

Apply Loop Family

For T

wo-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

Table of Contents

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

Table of Contents

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

Table of Contents

Other Loops

Repeat Loop Syntax

repeat statement

s

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() }

Table of Contents

Improving Speed Performance of LoopsLooping 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

Table of Contents

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

Table of Contents

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

Table of Contents

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 }

Table of Contents

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=...)

Table of Contents

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

Table of Contents

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

Table of Contents

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

Table of Contents

Useful Utilities

Debugging Utilities

Several debugging utilities are available for R. The most important utilities are: traceback(), browser(), options(error=recover), options(error=NULL) and debug(). The

Debugging in R

page 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"

Table of Contents

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"

Table of Contents

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"

Table of Contents

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"

Table of Contents

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

Table of Contents

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)

Table of Contents

Calling External Software with System CommandThe 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

Table of Contents

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

Table of Contents

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) }

Table of Contents

(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

Table of Content

Running R Programs

(1)

Executing an R script from the R console

source("my_script.R")

Table of Contents

(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

Table of Contents

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)

Table of Contents

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 Chambers

and

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) } } )

Table of Contents

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

Table of Contents

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 ...

Table of Contents

(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.

Table of Contents

(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"

Table of Contents

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" ...

Table of Contents

(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"))

Table of Contents

(H)

Functions to introspect classes

getClass("myclass")

getSlots("myclass")

slotNames("myclass")

extends("myclass2")

Assign Generics and MethodsAssign 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 ...

Table of Contents

(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 ...

Table of Contents

(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 ...

Table of Contents

(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 ...

Table of Contents

(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

Table of Contents

(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 ...

Table of Contents

(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)

Table of Contents

(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"))

Table of Contents

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

Table of Contents

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

Table of Contents

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)

Table of Contents

OS X:

install.packages("mypackage_1.0.tar.gz", repos=NULL, type="source")

Table of Contents

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)

Table of Contents

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

Table of Contents

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

Table of Contents

(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

Table of Contents

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")

Table of Contents

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")

Table of Contents

Sequence Analysis UtilitiesIncludes 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")

Table of Contents

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")

Table of Contents

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")

Table of Contents

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")

Table of Contents

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")

Table of Contents

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")

Table of Contents

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")

Table of Contents

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]])

Table of Contents

0 notes