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Introduction to R 2015

Workshop pages for students

Laptop Setup Instructions

Instructions for setting up your laptop can be found here: Laptop Setup Instructions

Difference Between R and R Studio

RStudio doesn’t know where libraries are installed, when they are not installed through the RStudio package manager. To tell RStudio the location, you can define the path in a startup file. Create a file called .Renviron . Inside there:

R_LIBS=<R Library Path of other installed packages>

That was the problem when students installed things in R Studio at the command line using the R command install.package().

… or you could use the package manger to install libraries.

Syntax highlighting

… of scripts in the R editor does not seem to work under Windows. If you want highlighted syntax, use RStudio instead. Or (seriously), get a Mac.

Helpful Materials

Day 1

Welcome

*Faculty: Michelle Brazas*

Module 1: First Steps

*Faculty: Boris Steipe*

Lecture:

2015_Intro_to_R.pdf
2015_Intro_to_R.mp4

Scripts:

Data:

Practical:

Resources:

Helpful links

Module 2: Programming Basics

*Faculty: Boris Steipe*

Practical:

Module 3: Using R for Data Analysis

*Faculty: Boris Steipe*

Scripts:

Resources:

Practical:

Code Scratchpad


?read.csv
rawDat <- read.csv("table_S3.csv",
                   header = FALSE,
                   stringsAsFactors = FALSE)
                   
head(rawDat, 10)
rawDat <- rawDat[-(1:6), ]
head(rawDat, 10)   # now note rownames problem
types <- c("genes",
           "B.ctrl",
           "B.LPS",
           "MF.ctrl",
           "MF.LPS",
           "NK.ctrl",
           "NK.LPS",
           "Mo.ctrl",
           "Mo.LPS",
           "pDC.ctrl",
           "pDC.LPS",
           "DC1.ctrl",
           "DC1.LPS",
           "DC2.ctrl",
           "DC2.LPS",
           "cluster")

colnames(rawDat) <- types

# Fix rownames problem
nrow(rawDat)
rownames(rawDat) <- 1:nrow(rawDat)

for (i in 2:ncol(rawDat)) {
  rawDat[,i] <- as.numeric(rawDat[ ,i])
}

typeInfo(rawDat)

filtering, preparing data for heatmap

sup3 <- read.csv("table_S3.csv",
                  skip = 6,
                  header = FALSE,
                  colClasses = c("character", rep("numeric", 15)),
                  col.names = c("genes",
                                  "B.ctrl", "B.LPS",
                                  "MF.ctrl", "MF.LPS",
                                  "NK.ctrl", "NK.LPS",
                                  "Mo.ctrl", "Mo.LPS",
                                  "pDC.ctrl", "pDC.LPS",
                                  "DC1.ctrl", "DC1.LPS",
                                  "DC2.ctrl", "DC2.LPS",
                                  "cluster"),
                  stringsAsFactors = FALSE)

summary(sup3[ ,2])
head(sup3)
dfMo <- abs(sup3[ ,"Mo.ctrl"] - sup3[ ,"Mo.LPS"]) 
summary(dfMo)

# example of order()
dfMo[1:5]
order(dfMo[1:5])
dfMo[order(dfMo[1:5])]

# for all genes ...
dfMoOrdered <- order(dfMo)
dfGenes <- tail(sup3[dfMoOrdered, 1], 10)

# convert to matrix
sup3M <- as.matrix(sup3[ ,2:15], ncol=14)
heatmap(sup3M)
View on GitHub