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XYomics (version 0.1.2)

generate_cat_report: Generate a Comprehensive Analysis Report

Description

This function creates an integrated report that combines key analysis outputs,

Usage

generate_cat_report(
  results_cat = results_cat,
  enrichment_cat = results_cat,
  grn_object = grn_object,
  output_file = "cat_analysis_report.html",
  output_dir = tempdir(),
  template_path = NULL,
  quiet = TRUE
)

Value

A character string with the path to the rendered report.

Arguments

results_cat

A data frame or list containing differential expression results.

enrichment_cat

A list with enrichment objects (e.g., BP, MF, KEGG, and optionally GSEA results).

grn_object

An igraph object representing the gene regulatory network (e.g., from PCSF analysis).

output_file

Character. The desired name (and optionally path) for the rendered report (default: "analysis_report.html").

output_dir

Character. Output directory to save the report to.

template_path

Character. Path to the R Markdown template file. If NULL, the function uses the built-in template located in inst/rmd/template_report.Rmd.

quiet

Logical. If TRUE (default), rendering will be quiet.