File size: 1,172 Bytes
a203fb4 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | # 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")
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