Introduction

paths <- list()

# Metadata
paths$patient_md <- file.path(PROJHOME, "metadata", "patient_metadata.tsv")
paths$mrna_md    <- file.path(PROJHOME, "metadata", "mrna_metadata.bams.tsv")
paths$tx2gene    <- file.path(
  PROJHOME, "reference", "GRCh38", "Sequence", "GencodeTranscriptome", "25",
  "gencode_v25_and_NC_007605.tx2gene.tsv")

# Results
paths$ebv_status <- file.path(PROJHOME, "results", "ebv_status", "ebv_status.txt")
paths$sex_status <- file.path(PROJHOME, "results", "sex_status", "sex_status.txt")
paths$salmon     <- file.path(PROJHOME, "results", "salmon")

# Set RNG seed for reproducibility
global_seed <- 87510475  # Generated by runif(1, 0, 10^8)
set.seed(global_seed)

# Use all available cores when multithreading
num_cores <- parallel::detectCores()
doMC::registerDoMC(cores = num_cores)

# Parameters for multiple test correction
p_adjust <- purrr::partial(p.adjust, method = "BH")
qmin     <- 0.1

# Effective genome size
genome_size <- 2934876451