| # Set working directory | |
| library(DESeq2) | |
| # Define directory for count files | |
| directory_sc <- "counts_sc/CYC8_30/" | |
| # List all count files (including both IAA and DMSO) | |
| files_sc <- list.files(directory_sc, pattern = "\\.txt$", full.names = FALSE) | |
| # Extract conditions from filenames: IAA as treated, DMSO as untreated | |
| condition <- ifelse(grepl("IAA", files_sc, ignore.case = TRUE), "treated", "untreated") | |
| # Extract sample names without the file extension | |
| names <- sub("(.*).txt", "\\1", files_sc) | |
| # Create sample table for DESeq2 | |
| sampleTable <- data.frame( | |
| sampleName = names, | |
| fileName = files_sc, | |
| condition = condition | |
| ) | |
| # Create DESeq2 dataset from HTSeq count files | |
| sc_data <- DESeqDataSetFromHTSeqCount( | |
| sampleTable = sampleTable, | |
| directory = directory_sc, | |
| design = ~ condition | |
| ) | |
| # Define the order of conditions for comparison (DMSO as untreated, IAA as treated) | |
| sc_data$condition <- factor(sc_data$condition, levels = c("untreated", "treated")) | |
| # Run DESeq2 analysis | |
| sc_data <- DESeq(sc_data) | |
| # Get differential expression results | |
| res <- results(sc_data) | |
| summary(res) | |
| # Save results as CSV | |
| write.csv(as.data.frame(res), file = "CYC8_30_test.csv") | |