# 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")