In eckartbindewald/bfxapps2: R Bioinformatics Applications

knitr::opts_chunk$set(echo = TRUE, message=FALSE)

The Bioconductor Package DESeq2

• DESeq2 is an R/Bioconductor package
• Provided by Michael Love and Raphael Irizarri

if (!require("DESeq2")) {
  BiocManager::install("DESeq2")
}
library(knitr) # for function "kable"

Downloading a Count Matrix

countfile_url <- "https://raw.githubusercontent.com/PacktPublishing/R-Bioinformatics-Cookbook/master/datasets/ch1/modencodefly_count_table.txt"
countfile <- "modencodefly_count_table.txt"
if (!file.exists(countfile)) {
 download.file(countfile_url,countfile)
}
count_dataframe <- readr::read_tsv(countfile)
kable(head(count_dataframe))

Converting the Data Frame to a Matrix

genes <- count_dataframe[['gene']]
count_dataframe[['gene']] <- NULL
count_matrix <- as.matrix(count_dataframe)
rownames(count_matrix) <- genes

Downloading Phenotype Data

phenofile_url <- "https://raw.githubusercontent.com/PacktPublishing/R-Bioinformatics-Cookbook/master/datasets/ch1/modencodefly_phenodata.txt"
phenofile <- "modencodefly_phenodata.txt"
if (!file.exists(phenofile)) {
 download.file(phenofile_url,phenofile)
}
pheno_data <- readr::read_table2(phenofile)
kable(head(pheno_data))

Specifying Experiments of Interest

experiments_of_interest <- c("L1Larvae", "L2Larvae")
columns_of_interest <- which( pheno_data[['stage']] %in%
experiments_of_interest )
counts_of_interest <- count_matrix[,columns_of_interest]
kable(head(counts_of_interest))

Create Factors Corresponding to Groups

library(magrittr)
grouping <- pheno_data[['stage']][columns_of_interest] %>%
forcats::as_factor()
grouping

Build the DESeq Object

library("DESeq2")
dds <- DESeqDataSetFromMatrix(countData = as.data.frame(counts_of_interest), 
                              colData = grouping,
                              design = ~ stage)

Perform Computation

dds <- DESeq(dds)

Extract Results

# res <- results(dds, contrast=c("stage","L2Larvae","L1Larvae"))
# head(res)

eckartbindewald/bfxapps2 documentation built on Feb. 6, 2025, 3:22 a.m.