Introduction to R

22 minute read

Overview

What is R?

R is a powerful statistical environment and programming language for the analysis and visualization of data. The associated Bioconductor and CRAN package repositories provide many additional R packages for statistical data analysis for a wide array of research areas. The R software is free and runs on all common operating systems.

Why Using R?

• Complete statistical environment and programming language
• Efficient functions and data structures for data analysis
• Powerful graphics
• Access to fast growing number of analysis packages
• Most widely used language in bioinformatics
• Is standard for data mining and biostatistical analysis
• Technical advantages: free, open-source, available for all OSs

Books and Documentation

• simpleR - Using R for Introductory Statistics (John Verzani, 2004) - URL
• Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Gentleman et al., 2005) - URL
• More on this see “Finding Help” section in UCR Manual - URL

R Working Environments

R Projects and Interfaces

Some R working environments with support for syntax highlighting and utilities to send code to the R console:

• RStudio/Posit Desktop: excellent choice for beginners (Cheat Sheets)
• RStudio/Posit Server: web-based UI for RStudio. Available at UCR via onDemand (old standalone web instance will be discontinued).
• RStudio/Posit Cloud: cloud-based RStudio Server
• Vim-R-Tmux: R working environment based on vim and tmux.
• Emacs (ESS add-on package)
• gedit, Rgedit, RKWard, Eclipse, Tinn-R, Notepad++, NppToR

Example: RStudio

New integrated development environment (IDE) for R. Highly functional for both beginners and advanced.

RStudio IDE

Some userful shortcuts: Ctrl+Enter (send code), Ctrl+Shift+C (comment/uncomment), Ctrl+1/2 (switch window focus)

Example: Nvim-R-Tmux

Terminal-based Working Environment for R: Nvim-R-Tmux.

Nvim-R-Tmux IDE for R

Install and usage instructions for Nvim-R are provided in this slide show and this tutorial. The most detailed instructions can be found on the Nvim-R_Tmux GitHub repos.

R Package Repositories

• CRAN (>14,000 packages) general data analysis - URL
• Bioconductor (>2,000 packages) bioscience data analysis - URL
• Omegahat (>90 packages) programming interfaces - URL
• RStudio packages - URL

Working routine for tutorials

This section provides a short overview of the standard working routine users should use to load R-based tutorials of this website into an R IDE (Nvim-R or RStudio). For Nvim-R on HPCC users can visit the Quick Demo slide here.

1. Download *.Rmd or *.R file. These so called source files are always linked on the top right corner of each tutorial. The ones for this tutorial are here. The file download can be accomplished via wget from the command-line or with the save function in a user’s web browser.

2. Load *.Rmd or *.R file in Neovim (Nvim-R) or RStudio.

3. Send code from code editor to R console by pushing space bar in Neovim (Nvim-R) or Ctrl + Enter in RStudio. In *.Rmd files the code lines are in so called code chunks and only those ones can be sent to the console. To obtain in Neovim a connected R session one has to initiate by pressing the \rf key combination. For details see here.

Installation of R, RStudio and R Packages

1. Install R for your operating system from CRAN.

2. Install RStudio from RStudio.

3. Install CRAN Packages from R console like this:

   install.packages(c("pkg1", "pkg2")) 
   install.packages("pkg.zip", repos=NULL)
   

4. Install Bioconductor packages as follows:

   if (!requireNamespace("BiocManager", quietly = TRUE))
       install.packages("BiocManager") # Installs BiocManager if not available yet
   BiocManager::version() # Reports Bioconductor version
   BiocManager::install(c("pkg1", "pkg2")) # Installs packages specified under "pkg1" 
   

5. For more details consult the Bioc Install page and BiocManager package.

6. Instructions for upgrading R and packages to newer versions are given at the end of this tutorial here.

Getting Around

Startup and Closing Behavior

• Starting R: The R GUI versions, including RStudio, under Windows and Mac OS X can be opened by double-clicking their icons. Alternatively, one can start it by typing R in a terminal (default under Linux).

• Startup/Closing Behavior: The R environment is controlled by hidden files in the startup directory: .RData, .Rhistory and .Rprofile (optional).

• Closing R:

q()  

Save workspace image? [y/n/c]:

• Note: When responding with y, then the entire R workspace will be written to the .RData file which can become very large. Often it is better to select n here, because a much better working pratice is to save an analysis protocol to an R or Rmd source file. This way one can quickly regenerate all data sets and objects needed in a future session.

Navigating directories

List objects in current R session

ls()

Return content of current working directory

dir()

Return path of current working directory

getwd()

Change current working directory

setwd("/home/user")

Basic Syntax

Create an object with the assignment operator <- or =

object <- ...

General R command syntax

object <- function_name(arguments) 
object <- object[arguments] 

Instead of the assignment operator one can use the assign function

assign("x", function(arguments))

To simplify chaining of serveral operations, dplyr (magrittr) provides the %>% (pipe) operator, where x %>% f(y) turns into f(x, y). This way one can pipe together multiple operations by writing them from left-to-right or top-to-bottom. This makes for easy to type and readable code. Details on this are provided in the dplyr tutorial here.

... %>% ...

Finding help

?function_name

Load a library/package

library("my_library") 

List functions defined by a library

library(help="my_library")

Load library manual (PDF or HTML file)

vignette("my_library") 

Execute an R script from within R

source("my_script.R")

Execute an R script from command-line (the first of the three options is preferred)

$ Rscript my_script.R
$ R CMD BATCH my_script.R 
$ R --slave < my_script.R 

Data Types

Numeric data

Example: 1, 2, 3, ...

x <- c(1, 2, 3)
x

## [1] 1 2 3

is.numeric(x)

## [1] TRUE

as.character(x)

## [1] "1" "2" "3"

Character data

Example: "a", "b", "c", ...

x <- c("1", "2", "3")
x

## [1] "1" "2" "3"

is.character(x)

## [1] TRUE

as.numeric(x)

## [1] 1 2 3

Complex data

Example: mix of both

c(1, "b", 3)

## [1] "1" "b" "3"

Logical data

Example: TRUE of FALSE

x <- 1:10 < 5
x  

##  [1]  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE

!x

##  [1] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE

which(x) # Returns index for the 'TRUE' values in logical vector

## [1] 1 2 3 4

Data Objects

Object types

• List of common object types
  • vectors: ordered collection of numeric, character, complex and logical values.
  • factors: special type vectors with grouping information of its components
  • data.frames including modern variants DataFrame, tibbles, etc.: two dimensional structures with different data types
  • matrices: two dimensional structures with data of same type
  • arrays: multidimensional arrays of vectors
  • lists: general form of vectors with different types of elements
  • functions: piece of code
  • Many more …
• Simple rules for naming objects and their components
  • Object, row and column names should not start with a number
  • Avoid spaces in object, row and column names
  • Avoid special characters like ‘#’

Vectors (1D)

Definition: numeric or character

myVec <- 1:10; names(myVec) <- letters[1:10]  
myVec <- setNames(1:10, letters[1:10]) # Same as above in single step
myVec[1:5]

## a b c d e 
## 1 2 3 4 5

myVec[c(2,4,6,8)]

## b d f h 
## 2 4 6 8

myVec[c("b", "d", "f")]

## b d f 
## 2 4 6

Factors (1D)

Definition: vectors with grouping information

factor(c("dog", "cat", "mouse", "dog", "dog", "cat"))

## [1] dog   cat   mouse dog   dog   cat  
## Levels: cat dog mouse

Matrices (2D)

Definition: two dimensional structures with data of same type

myMA <- matrix(1:30, 3, 10, byrow = TRUE) 
class(myMA)

## [1] "matrix" "array"

myMA[1:2,]

##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
## [1,]    1    2    3    4    5    6    7    8    9    10
## [2,]   11   12   13   14   15   16   17   18   19    20

myMA[1, , drop=FALSE]

##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
## [1,]    1    2    3    4    5    6    7    8    9    10

Data Frames (2D)

Definition: data.frames are two dimensional objects with data of variable types

myDF <- data.frame(Col1=1:10, Col2=10:1) 
myDF[1:2, ]

##   Col1 Col2
## 1    1   10
## 2    2    9

Tibbles

Tibbles are a more modern version of data.frames. Among many other advantages, one can see here that tibbles have a nicer printing bahavior. Much more detailed information on this object class is provided in the dplyr/tidyverse manual section.

library(tidyverse)
as_tibble(iris)

## # A tibble: 150 × 5
##    Sepal.Length Sepal.Width Petal.Length Petal.Width Species
##           <dbl>       <dbl>        <dbl>       <dbl> <fct>  
##  1          5.1         3.5          1.4         0.2 setosa 
##  2          4.9         3            1.4         0.2 setosa 
##  3          4.7         3.2          1.3         0.2 setosa 
##  4          4.6         3.1          1.5         0.2 setosa 
##  5          5           3.6          1.4         0.2 setosa 
##  6          5.4         3.9          1.7         0.4 setosa 
##  7          4.6         3.4          1.4         0.3 setosa 
##  8          5           3.4          1.5         0.2 setosa 
##  9          4.4         2.9          1.4         0.2 setosa 
## 10          4.9         3.1          1.5         0.1 setosa 
## # … with 140 more rows

Note: The above example uses the iris test dataset that is available in every R installation without explicitly importing or loading it. The following examples will often make use of this dataset.

Arrays

Definition: data structure with one, two or more dimensions

Lists

Definition: containers for any object type

myL <- list(name="Fred", wife="Mary", no.children=3, child.ages=c(4,7,9)) 
myL

## $name
## [1] "Fred"
## 
## $wife
## [1] "Mary"
## 
## $no.children
## [1] 3
## 
## $child.ages
## [1] 4 7 9

myL[[4]][1:2] 

## [1] 4 7

Functions

Definition: piece of code

myfct <- function(arg1, arg2, ...) { 
	function_body 
}

Subsetting of data objects

(1.) Subsetting by positive or negative index/position numbers

myVec <- 1:26; names(myVec) <- LETTERS 
myVec[1:4]

## A B C D 
## 1 2 3 4

(2.) Subsetting by same length logical vectors

myLog <- myVec > 10
myVec[myLog] 

##  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 
## 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

(3.) Subsetting by field names

myVec[c("B", "K", "M")]

##  B  K  M 
##  2 11 13

(4.) Subset with $ sign: references a single column or list component by its name

iris$Species[1:8]

## [1] setosa setosa setosa setosa setosa setosa setosa setosa
## Levels: setosa versicolor virginica

Important Utilities

Combining Objects

The c function combines vectors and lists

c(1, 2, 3)

## [1] 1 2 3

x <- 1:3; y <- 101:103
c(x, y)

## [1]   1   2   3 101 102 103

The cbind and rbind functions can be used to append columns and rows, respecively.

ma <- cbind(x, y)
ma

##      x   y
## [1,] 1 101
## [2,] 2 102
## [3,] 3 103

rbind(ma, ma)

##      x   y
## [1,] 1 101
## [2,] 2 102
## [3,] 3 103
## [4,] 1 101
## [5,] 2 102
## [6,] 3 103

Accessing Dimensions of Objects

Length and dimension information of objects

length(iris$Species)

## [1] 150

dim(iris)

## [1] 150   5

Accessing Name Slots of Objects

Accessing row and column names of 2D objects

rownames(iris)[1:8]

## [1] "1" "2" "3" "4" "5" "6" "7" "8"

colnames(iris)

## [1] "Sepal.Length" "Sepal.Width"  "Petal.Length" "Petal.Width"  "Species"

Return name field of vectors and lists

names(myVec)

##  [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X"
## [25] "Y" "Z"

names(myL)

## [1] "name"        "wife"        "no.children" "child.ages"

Sorting Objects

The function sort returns a vector in ascending or descending order.

sort(10:1)

##  [1]  1  2  3  4  5  6  7  8  9 10

The function order returns a sorting index for sorting an object alphanumerically.

sortindex <- order(iris[,1], decreasing = FALSE)
sortindex[1:12]

##  [1] 14  9 39 43 42  4  7 23 48  3 30 12

iris[sortindex,][1:2,]

##    Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 14          4.3         3.0          1.1         0.1  setosa
## 9           4.4         2.9          1.4         0.2  setosa

sortindex <- order(-iris[,1]) # Same as decreasing=TRUE

Sorting multiple columns

iris[order(iris$Sepal.Length, iris$Sepal.Width),][1:2,]

##    Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 14          4.3         3.0          1.1         0.1  setosa
## 9           4.4         2.9          1.4         0.2  setosa

Operators and Calculations

Comparison Operators

Comparison operators: ==, !=, <, >, <=, >=

1==1

## [1] TRUE

Logical operators for boolean operations: AND: &, OR: |, NOT: !

x <- 1:10; y <- 10:1
x > y & x > 5

##  [1] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE

Basic Calculations

To look up math functions, see Function Index here

x + y

##  [1] 11 11 11 11 11 11 11 11 11 11

sum(x)

## [1] 55

mean(x)

## [1] 5.5

apply(iris[1:6,1:3], 1, mean) 

##        1        2        3        4        5        6 
## 3.333333 3.100000 3.066667 3.066667 3.333333 3.666667

Reading and Writing External Data

Import of tabular data

Import of a tab-delimited tabular file

myDF <- read.delim("myData.xls", sep="\t")

Import of Google Sheets. The following example imports a sample Google Sheet from here. Detailed instructions for interacting from R with Google Sheets with the required googlesheets4 package are here.

library(googlesheets4)
gs4_deauth() # Easiest method for reading public access sheets
mysheet <- read_sheet("1U-32UcwZP1k3saKeaH1mbvEAOfZRdNHNkWK2GI1rpPM", skip=4)
myDF <- as.data.frame(mysheet)
myDF

Import from Excel sheets works well with readxl. For details see the readxl package manual here. Note: working with tab- or comma-delimited files is more flexible and highly preferred for automated analysis workflows.

library("readxl")
mysheet <- read_excel(targets_path, sheet="Sheet1")

Additional import functions are described in the readr package section here.

Export of tabular data

write.table(myDF, file="myfile.xls", sep="\t", quote=FALSE, col.names=NA)

Line-wise import

myDF <- readLines("myData.txt")

Line-wise export

writeLines(month.name, "myData.txt")

Export R object

mylist <- list(C1=iris[,1], C2=iris[,2]) # Example to export
saveRDS(mylist, "mylist.rds")

Import R object

mylist <- readRDS("mylist.rds")

Copy and paste into R

On Windows/Linux systems

read.delim("clipboard") 

On Mac OS X systems

read.delim(pipe("pbpaste")) 

Copy and paste from R

On Windows/Linux systems

write.table(iris, "clipboard", sep="\t", col.names=NA, quote=FALSE) 

On Mac OS X systems

zz <- pipe('pbcopy', 'w')
write.table(iris, zz, sep="\t", col.names=NA, quote=FALSE)
close(zz) 

Homework 3A

Homework 3A: Object Subsetting Routines and Import/Export

Useful R Functions

Unique entries

Make vector entries unique with unique

length(iris$Sepal.Length)

## [1] 150

length(unique(iris$Sepal.Length))

## [1] 35

Count occurrences

Count occurrences of entries with table

table(iris$Species)

## 
##     setosa versicolor  virginica 
##         50         50         50

Aggregate data

Compute aggregate statistics with aggregate

aggregate(iris[,1:4], by=list(iris$Species), FUN=mean, na.rm=TRUE)

##      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

Intersect data

Compute intersect between two vectors with %in%

month.name %in% c("May", "July")

##  [1] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE

Merge data frames

Join two data frames by common field entries with merge (here row names by.x=0). To obtain only the common rows, change all=TRUE to all=FALSE. To merge on specific columns, refer to them by their position numbers or their column names.

frame1 <- iris[sample(1:length(iris[,1]), 30), ]
frame1[1:2,]

##     Sepal.Length Sepal.Width Petal.Length Petal.Width   Species
## 147          6.3         2.5          5.0         1.9 virginica
## 49           5.3         3.7          1.5         0.2    setosa

dim(frame1)

## [1] 30  5

my_result <- merge(frame1, iris, by.x = 0, by.y = 0, all = TRUE)
dim(my_result)

## [1] 150  11

Graphics in R

Advantages

• Powerful environment for visualizing scientific data
• Integrated graphics and statistics infrastructure
• Publication quality graphics
• Fully programmable
• Highly reproducible
• Full LaTeX and Markdown support via knitr and R markdown
• Vast number of R packages with graphics utilities

Documentation for R Graphics

General

• Graphics Task Page - URL
• R Graph Gallery - URL
• R Graphical Manual - URL
• Paul Murrell’s book R (Grid) Graphics - URL

Interactive graphics

• rggobi` (GGobi) - URL
• iplots - URL
• Open GL (rgl) - URL

Graphics Environments

Viewing and saving graphics in R

• On-screen graphics
• postscript, pdf, svg
• jpeg, png, wmf, tiff, …

Four major graphic environments

1. Low-level infrastructure

• R Base Graphics (low- and high-level)
• grid: Manual

2. High-level infrastructure \begin{itemize}

• lattice: Manual, Intro, Book
• ggplot2: Manual, Intro, Book

Base Graphics: Overview

Important high-level plotting functions

• plot: generic x-y plotting
• barplot: bar plots
• boxplot: box-and-whisker plot
• hist: histograms
• pie: pie charts
• dotchart: cleveland dot plots
• image, heatmap, contour, persp: functions to generate image-like plots
• qqnorm, qqline, qqplot: distribution comparison plots
• pairs, coplot: display of multivariant data

Help on graphics functions

• ?myfct
• ?plot
• ?par

Preferred Object Types

• Matrices and data frames
• Vectors
• Named vectors

Scatter Plots

Basic Scatter Plot

Sample data set for subsequent plots

set.seed(1410)
y <- matrix(runif(30), ncol=3, dimnames=list(letters[1:10], LETTERS[1:3]))

Plot data

plot(y[,1], y[,2]) 

All pairs

pairs(y) 

With labels

plot(y[,1], y[,2], pch=20, col="red", main="Symbols and Labels")
text(y[,1]+0.03, y[,2], rownames(y))

More examples

Print instead of symbols the row names

plot(y[,1], y[,2], type="n", main="Plot of Labels")
text(y[,1], y[,2], rownames(y)) 

Usage of important plotting parameters

grid(5, 5, lwd = 2) 
op <- par(mar=c(8,8,8,8), bg="lightblue")
plot(y[,1], y[,2], type="p", col="red", cex.lab=1.2, cex.axis=1.2, 
     cex.main=1.2, cex.sub=1, lwd=4, pch=20, xlab="x label", 
     ylab="y label", main="My Main", sub="My Sub")
par(op)

Important arguments

• mar: specifies the margin sizes around the plotting area in order: c(bottom, left, top, right)
• col: color of symbols
• pch: type of symbols, samples: example(points)
• lwd: size of symbols
• cex.*: control font sizes
• For details see ?par

Add regression line

plot(y[,1], y[,2])
myline <- lm(y[,2]~y[,1]); abline(myline, lwd=2) 

summary(myline) 

## 
## Call:
## lm(formula = y[, 2] ~ y[, 1])
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.40357 -0.17912 -0.04299  0.22147  0.46623 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)  
## (Intercept)   0.5764     0.2110   2.732   0.0258 *
## y[, 1]       -0.3647     0.3959  -0.921   0.3839  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.3095 on 8 degrees of freedom
## Multiple R-squared:  0.09589,	Adjusted R-squared:  -0.01712 
## F-statistic: 0.8485 on 1 and 8 DF,  p-value: 0.3839

Log scale

Same plot as above, but on log scale

plot(y[,1], y[,2], log="xy") 

Add a mathematical expression

plot(y[,1], y[,2]); text(y[1,1], y[1,2], expression(sum(frac(1,sqrt(x^2*pi)))), cex=1.3) 

Homework 3B

Homework 3B: Scatter Plots

Line Plots

Single data set

plot(y[,1], type="l", lwd=2, col="blue") 

Many Data Sets

Plots line graph for all columns in data frame y. The split.screen function is used in this example in a for loop to overlay several line graphs in the same plot.

split.screen(c(1,1)) 

## [1] 1

plot(y[,1], ylim=c(0,1), xlab="Measurement", ylab="Intensity", type="l", lwd=2, col=1)
for(i in 2:length(y[1,])) { 
	screen(1, new=FALSE)
	plot(y[,i], ylim=c(0,1), type="l", lwd=2, col=i, xaxt="n", yaxt="n", ylab="", xlab="", main="", bty="n") 
}

close.screen(all=TRUE) 

Bar Plots

Basics

barplot(y[1:4,], ylim=c(0, max(y[1:4,])+0.3), beside=TRUE, legend=letters[1:4]) 
text(labels=round(as.vector(as.matrix(y[1:4,])),2), x=seq(1.5, 13, by=1) + sort(rep(c(0,1,2), 4)), y=as.vector(as.matrix(y[1:4,]))+0.04) 

Error Bars

bar <- barplot(m <- rowMeans(y) * 10, ylim=c(0, 10))
stdev <- sd(t(y))
arrows(bar, m, bar, m + stdev, length=0.15, angle = 90)

Histograms

hist(y, freq=TRUE, breaks=10)

Density Plots

plot(density(y), col="red")

Pie Charts

pie(y[,1], col=rainbow(length(y[,1]), start=0.1, end=0.8), clockwise=TRUE)
legend("topright", legend=row.names(y), cex=1.3, bty="n", pch=15, pt.cex=1.8, 
col=rainbow(length(y[,1]), start=0.1, end=0.8), ncol=1) 

Color Selection Utilities

Default color palette and how to change it

palette()

## [1] "black"   "#DF536B" "#61D04F" "#2297E6" "#28E2E5" "#CD0BBC" "#F5C710" "gray62"

palette(rainbow(5, start=0.1, end=0.2))
palette()

## [1] "#FF9900" "#FFBF00" "#FFE600" "#F2FF00" "#CCFF00"

palette("default")

The gray function allows to select any type of gray shades by providing values from 0 to 1

gray(seq(0.1, 1, by= 0.2))

## [1] "#1A1A1A" "#4D4D4D" "#808080" "#B3B3B3" "#E6E6E6"

Color gradients with colorpanel function from gplots library`

library(gplots)
colorpanel(5, "darkblue", "yellow", "white")

## [1] "#00008B" "#808046" "#FFFF00" "#FFFF80" "#FFFFFF"

Much more on colors in R see Earl Glynn’s color chart here

Saving Graphics to File

After the pdf() command all graphs are redirected to file test.pdf. Works for all common formats similarly: jpeg, png, ps, tiff, …

pdf("test.pdf")
plot(1:10, 1:10)
dev.off() 

Generates Scalable Vector Graphics (SVG) files that can be edited in vector graphics programs, such as InkScape.

library("RSvgDevice")
devSVG("test.svg")
plot(1:10, 1:10)
dev.off() 

Homework 3C

Homework 3C: Bar Plots

Analysis Routine

Overview

The following exercise introduces a variety of useful data analysis utilities in R.

Analysis Routine: Data Import

• Step 1: To get started with this exercise, direct your R session to a dedicated workshop directory and download into this directory the following sample tables. Then import the files into Excel and save them as tab delimited text files.

  • MolecularWeight_tair7.xls
  • TargetP_analysis_tair7.xls

Import the tables into R

Import molecular weight table

my_mw <- read.delim(file="MolecularWeight_tair7.xls", header=TRUE, sep="\t") 
my_mw[1:2,]

Import subcelluar targeting table

my_target <- read.delim(file="TargetP_analysis_tair7.xls", header=TRUE, sep="\t") 
my_target[1:2,]

Online import of molecular weight table

my_mw <- read.delim(file="http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/Samples/MolecularWeight_tair7.xls", header=TRUE, sep="\t") 
my_mw[1:2,]

##   Sequence.id Molecular.Weight.Da. Residues
## 1 AT1G08520.1                83285      760
## 2 AT1G08530.1                27015      257

Online import of subcelluar targeting table

my_target <- read.delim(file="http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/Samples/TargetP_analysis_tair7.xls", header=TRUE, sep="\t") 
my_target[1:2,]

##      GeneName Loc   cTP   mTP    SP other
## 1 AT1G08520.1   C 0.822 0.137 0.029 0.039
## 2 AT1G08530.1   C 0.817 0.058 0.010 0.100

Merging Data Frames

• Step 2: Assign uniform gene ID column titles

colnames(my_target)[1] <- "ID"
colnames(my_mw)[1] <- "ID" 

• Step 3: Merge the two tables based on common ID field

my_mw_target <- merge(my_mw, my_target, by.x="ID", by.y="ID", all.x=TRUE)

• Step 4: Shorten one table before the merge and then remove the non-matching rows (NAs) in the merged file

my_mw_target2a <- merge(my_mw, my_target[1:40,], by.x="ID", by.y="ID", all.x=TRUE)  # To remove non-matching rows, use the argument setting 'all=FALSE'.
my_mw_target2 <- na.omit(my_mw_target2a) # Removes rows containing "NAs" (non-matching rows).

• Homework 3D: How can the merge function in the previous step be executed so that only the common rows among the two data frames are returned? Prove that both methods - the two step version with na.omit and your method - return identical results.
• Homework 3E: Replace all NAs in the data frame my_mw_target2a with zeros.

Filtering Data

• Step 5: Retrieve all records with a value of greater than 100,000 in ‘MW’ column and ‘C’ value in ‘Loc’ column (targeted to chloroplast).

query <- my_mw_target[my_mw_target[, 2] > 100000 & my_mw_target[, 4] == "C", ] 
query[1:4, ]

##              ID Molecular.Weight.Da. Residues Loc   cTP   mTP    SP other
## 219 AT1G02730.1               132588     1181   C 0.972 0.038 0.008 0.045
## 243 AT1G02890.1               136825     1252   C 0.748 0.529 0.011 0.013
## 281 AT1G03160.1               100732      912   C 0.871 0.235 0.011 0.007
## 547 AT1G05380.1               126360     1138   C 0.740 0.099 0.016 0.358

dim(query)

## [1] 170   8

• Homework 3F: How many protein entries in the my_mw_target data frame have a MW of greater then 4,000 and less then 5,000. Subset the data frame accordingly and sort it by MW to check that your result is correct.

String Substitutions

• Step 6: Use a regular expression in a substitute function to generate a separate ID column that lacks the gene model extensions.

my_mw_target3 <- data.frame(loci=gsub("\\..*", "", as.character(my_mw_target[,1]), perl = TRUE), my_mw_target)
my_mw_target3[1:3,1:8]

##        loci          ID Molecular.Weight.Da. Residues Loc  cTP   mTP    SP
## 1 AT1G01010 AT1G01010.1                49426      429   _ 0.10 0.090 0.075
## 2 AT1G01020 AT1G01020.1                28092      245   * 0.01 0.636 0.158
## 3 AT1G01020 AT1G01020.2                21711      191   * 0.01 0.636 0.158

• Homework 3G: Retrieve those rows in my_mw_target3 where the second column contains the following identifiers: c("AT5G52930.1", "AT4G18950.1", "AT1G15385.1", "AT4G36500.1", "AT1G67530.1"). Use the %in% function for this query. As an alternative approach, assign the second column to the row index of the data frame and then perform the same query again using the row index. Explain the difference of the two methods.

Calculations on Data Frames

• Step 7: Count the number of duplicates in the loci column with the table function and append the result to the data frame with the cbind function.

mycounts <- table(my_mw_target3[,1])[my_mw_target3[,1]]
my_mw_target4 <- cbind(my_mw_target3, Freq=mycounts[as.character(my_mw_target3[,1])]) 

• Step 8: Perform a vectorized devision of columns 3 and 4 (average AA weight per protein)

data.frame(my_mw_target4, avg_AA_WT=(my_mw_target4[,3] / my_mw_target4[,4]))[1:2,] 

##        loci          ID Molecular.Weight.Da. Residues Loc  cTP   mTP    SP other Freq.Var1
## 1 AT1G01010 AT1G01010.1                49426      429   _ 0.10 0.090 0.075 0.925 AT1G01010
## 2 AT1G01020 AT1G01020.1                28092      245   * 0.01 0.636 0.158 0.448 AT1G01020
##   Freq.Freq avg_AA_WT
## 1         1  115.2121
## 2         2  114.6612

• Step 9: Calculate for each row the mean and standard deviation across several columns

mymean <- apply(my_mw_target4[,6:9], 1, mean)
mystdev <- apply(my_mw_target4[,6:9], 1, sd, na.rm=TRUE)
data.frame(my_mw_target4, mean=mymean, stdev=mystdev)[1:2,5:12] 

##   Loc  cTP   mTP    SP other Freq.Var1 Freq.Freq   mean
## 1   _ 0.10 0.090 0.075 0.925 AT1G01010         1 0.2975
## 2   * 0.01 0.636 0.158 0.448 AT1G01020         2 0.3130

Plotting Example

• Step 10: Generate scatter plot columns: ‘MW’ and ‘Residues’

plot(my_mw_target4[1:500,3:4], col="red")

Export Results and Run Entire Exercise as Script

• Step 11: Write the data frame my_mw_target4 into a tab-delimited text file and inspect it in Excel.

write.table(my_mw_target4, file="my_file.xls", quote=FALSE, sep="\t", col.names = NA) 

• Homework 3H: Write all commands from this exercise into an R script named exerciseRbasics.R, or download it from here. Then execute the script with the source function like this: source("exerciseRbasics.R"). This will run all commands of this exercise and generate the corresponding output files in the current working directory. For homework 3H it is not necessary to submit the result files generated by the exerciseRbasics.R script. Stating how the script was executed (e.g. source or Rscript command) will be sufficient.

source("exerciseRbasics.R")

Or run it from the command-line (not from R!) with Rscript like this:

Rscript exerciseRbasics.R

Miscellaneous Topics

Upgrading to New R/Bioc Versions

When upgrading to a new R version, it is important to understand that a reinstall of all R packages is necessary because CRAN/Bioc packages are developed and tested for specific R versions. This means when upgrading R, then the corresponding packages need to be upgraded to the versions that match the new R version. The following steps will work in many situations.

1. Export a list of all packages installed in a current version of R to a file (below named my_R_pkgs.txt) by running the following commands from within R (or use Rscript -e from command-line)

   my_R_pkgs <- rownames(installed.packages())
   writeLines(my_R_pkgs, "my_R_pkgs.txt")
   

2. Install new version of R, and then from within the new R version all packages one had installed before. The first install command below installs first a series of packages that are useful to have in general no matter what. Custom packages are then installed in the next lines. Note, this can only install packages from CRAN and Bioconductor. Packages from custom sources, including private GitHub accounts, need to be installed separately. Usually, one can identify them by the report generated at the end of the below install routine telling which packages are not available on CRAN or Bioconductor.

   install.packages(c("devtools", "tidyverse", "BiocManager"))
   BiocManager::install(version = "3.17") # look up current Bioc version here: https://bit.ly/3NADnll
   my_R_pkgs <- readLines("my_R_pkgs.txt")
   BiocManager::install(my_R_pkgs)
   

Session Info

sessionInfo()

## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 10 (buster)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
##  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
## [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] gplots_3.1.1     forcats_0.5.1    stringr_1.4.0    dplyr_1.0.7      purrr_0.3.4     
##  [6] readr_2.1.1      tidyr_1.1.4      tibble_3.1.6     tidyverse_1.3.1  ggplot2_3.3.5   
## [11] limma_3.50.0     BiocStyle_2.22.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8.3        lubridate_1.8.0     gtools_3.9.2        assertthat_0.2.1   
##  [5] digest_0.6.29       utf8_1.2.2          R6_2.5.1            cellranger_1.1.0   
##  [9] backports_1.4.0     reprex_2.0.1        evaluate_0.15       highr_0.9          
## [13] httr_1.4.2          blogdown_1.8.2      pillar_1.6.4        rlang_1.0.2        
## [17] readxl_1.3.1        rstudioapi_0.13     jquerylib_0.1.4     rmarkdown_2.13     
## [21] munsell_0.5.0       broom_0.7.10        compiler_4.1.3      modelr_0.1.8       
## [25] xfun_0.30           pkgconfig_2.0.3     htmltools_0.5.2     tidyselect_1.1.1   
## [29] bookdown_0.25       codetools_0.2-18    fansi_0.5.0         crayon_1.4.2       
## [33] tzdb_0.2.0          dbplyr_2.1.1        withr_2.4.3         bitops_1.0-7       
## [37] grid_4.1.3          jsonlite_1.8.0      gtable_0.3.0        lifecycle_1.0.1    
## [41] DBI_1.1.1           magrittr_2.0.2      scales_1.1.1        KernSmooth_2.23-20 
## [45] cli_3.1.0           stringi_1.7.6       fs_1.5.2            xml2_1.3.3         
## [49] bslib_0.3.1         ellipsis_0.3.2      generics_0.1.1      vctrs_0.3.8        
## [53] tools_4.1.3         glue_1.6.2          hms_1.1.1           fastmap_1.1.0      
## [57] yaml_2.3.5          colorspace_2.0-2    BiocManager_1.30.16 caTools_1.18.2     
## [61] rvest_1.0.2         knitr_1.37          haven_2.4.3         sass_0.4.0

References