Run Quality Control Pipeline — run_qc

This function runs the quality control portion of the RNA-seq analysis pipeline, including filtering genes, generating QC plots, and saving expression data.

Usage

run_qc_pip(
  dds,
  org,
  remove_xy = TRUE,
  remove_mt = TRUE,
  group_by,
  quantile = 0.05,
  save_dir = getwd(),
  save_dir_name = "qc_results"
)

Arguments

dds: DESeq2 object containing the expression data
org: The organism to use, either "human" or "mouse".
remove_xy: Logical. If TRUE, removes genes on X and Y chromosomes. Default is TRUE
remove_mt: Logical. If TRUE, removes mitochondrial genes. Default is TRUE
group_by: Column name in colData(dds) to use for grouping.
quantile: Quantile threshold for filtering lowly expressed genes. Default is 0.05
save_dir: Directory where all output files will be saved. Default is current working directory
save_dir_name: Name of the subdirectory to save files in. Default is "qc_results"

Value

The processed DESeq2 object

Examples

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

# Run QC pipeline with custom settings
dds <- run_qc_pip(dds, org = "mouse", remove_xy = TRUE, save_dir_name = "custom_results")
} # }