#!/usr/bin/env Rscript

suppressPackageStartupMessages({
    library(data.table)
})

setDTthreads(8)

# =====================================================
# INPUT
# =====================================================

infile <-
"/BLUES/eric/ONT_WGBS/Heatmap/RNAseq_matrix_FULL_log2FPKMp1_no_rRNA_tRNA.tsv"

# =====================================================
# OUTPUT
# =====================================================

outdir <- "/BLUES/eric/ONT_WGBS/Figure_5/MA_plot"
dir.create(outdir, showWarnings = FALSE, recursive = TRUE)

outfile <-
file.path(outdir,
          "RNAseq_log2FC.tsv")

# =====================================================
# LOAD
# =====================================================

dt <- fread(infile)

# =====================================================
# TRUE log2FC
# =====================================================

dt[, mean_expression_NP := (Naive + Primed) / 2]
dt[, mean_expression_TN := (TSC + Naive) / 2]

dt[, log2FC_NP := Naive - Primed]
dt[, log2FC_TN := TSC - Naive]

# =====================================================
# OUTPUT
# =====================================================

out <- dt[, .(
    subfamily,
    Primed,
    Naive,
    TSC,
    mean_expression_NP,
    log2FC_NP,
    mean_expression_TN,
    log2FC_TN
)]

fwrite(
    out,
    outfile,
    sep = "\t",
    quote = FALSE
)

cat("Wrote:", outfile, "\n")
cat("Rows:", nrow(out), "\n")