Run Sample Distance Pipeline — run_dist

This function runs the distance analysis portion of the RNA-seq analysis pipeline, including generating PCA and distance plots, and saving distance data.

Usage

run_dist_pip(
  dds,
  group_by,
  pals = NULL,
  batch = NULL,
  save_dir = getwd(),
  save_dir_name = "qc_results"
)

Arguments

dds: DESeq2 object containing the expression data
group_by: Column name in colData(dds) to use for grouping. Default is "Group1"
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
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 distance pipeline with default settings
dds <- run_dist_pip(dds)

# Run distance pipeline with custom settings and batch correction
dds <- run_dist_pip(dds, batch = "Batch", save_dir_name = "qc_results")
} # }