DESeq2

#!/usr/bin/R

library(tximport)
library(readr)
library('tximportData')

dir <- '/home/prabat/dwhelper/1/quants/quants'
dir_quants <- '/home/prabat/dwhelper/1/quants'
setwd(dir)

samples <- read.csv('SraRunTable_1.csv', header = T)
samples
samples$condition <- factor(rep(c('control', 'saline'), each = 9))
rownames(samples) <- samples$Run_s
samples

files <- file.path(dir_quants, samples$Run_s, 'quant.sf')
names(files) <- samples$Run_s
names(files)

tx2gene <- read.csv('tx2gene.csv')
head(tx2gene)

txi <- tximport(files, type = 'salmon', tx2gene = tx2gene[c(2,3)])

library('DESeq2')
ddsTxi <- DESeqDataSetFromTximport(txi,
                                   colData = samples,
                                   design = ~ condition)

ddsTxi

dds <- ddsTxi[rowSums(counts(ddsTxi)) > 1]

dds$condition <- factor(dds$condition, levels=c("control", "saline"))

dds <- DESeq(dds)
res <- results(dds)

resultsNames(dds)
resLFC <- lfcShrink(dds, coef = 2, res = res)

resOrdered <- res[order(res$padj),]
resOrdered

summary(res)

head(res)

write.csv(as.data.frame(resOrdered), file = 'salinity_treated_results.csv')