Run Complete RNA-seq Pipeline — run_rna

This function runs a complete RNA-seq analysis pipeline including quality control, differential expression analysis, and gene set enrichment analysis for all possible comparisons in the experiment. It generates various plots and saves results in organized directories.

Usage

run_rna_pip(
  dds,
  org,
  group_by,
  remove_xy = FALSE,
  remove_mt = FALSE,
  quantile = 0.05,
  pals = NULL,
  batch = NULL,
  order = "pxfc",
  save_dir = getwd()
)

Arguments

dds: DESeq2 object
org: The organism to use, either "human" or "mouse".
group_by: Column name in colData(dds) to use for grouping.
remove_xy: Logical. If TRUE, removes genes on X and Y chromosomes. Default is FALSE
remove_mt: Logical. If TRUE, removes mitochondrial genes. Default is FALSE
quantile: Quantile threshold for filtering lowly expressed genes. Default is 0.05
pals: Vector of colors to use for groups. If NULL, uses default ggplot2 colors. Default is NULL
batch: Column name in colData(dds) to use for batch correction. Default is NULL
order: Column name to use for ranking genes. Default is "pxfc"
save_dir: Directory where all output files will be saved. Default is current working directory

Value

The processed DESeq2 object

Examples

if (FALSE) { # \dontrun{
# Run complete pipeline with default settings
dds <- run_rna_pip(dds)

# Run pipeline with custom settings
dds <- run_rna_pip(dds, 
                   org = "mouse", 
                   remove_xy = TRUE,
                   group_by = "Treatment",
                   save_dir = "output")

# Run pipeline with batch correction
dds <- run_rna_pip(dds, batch = "Batch")
} # }