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Generate a reproducible analysis report

Source: R/08_report.R
mx_report.Rd

Renders an HTML (or PDF) report with methods text, study table, fold-change concordance, volcano plot, top-gene table with confidence and prediction intervals, heterogeneity, forest plots, leave-one-out robustness, pathway results (if present) and session information.

Usage

mx_report(
  meta_result,
  de_results,
  studies = NULL,
  format = c("html", "pdf"),
  output_dir = ".",
  output_file = "metaXpress_report",
  padj_threshold = 0.05,
  lfc_threshold = 0
)

Arguments

meta_result

A metaXpressResult object from mx_meta.

de_results

The named list of per-study DE data.frames (or metaXpressStudy objects) used for the meta-analysis.

studies

Optional list of metaXpressStudy objects (currently unused; kept for API compatibility).

format

"html" (default) or "pdf" (requires LaTeX).

output_dir

Output directory. Default: ".".

output_file

File name without extension. Default: "metaXpress_report".

padj_threshold, lfc_threshold

Significance thresholds used in the report. Defaults: 0.05 and 0.

Value

The path to the generated report (invisibly).

See also

mx_export, mx_session_info

Examples

# \donttest{
if (rmarkdown::pandoc_available()) {
  ad <- readRDS(system.file("extdata", "ad_brain_de.rds",
                            package = "metaXpress"))
  res <- mx_meta(ad$de_results)
  mx_report(res, ad$de_results, output_dir = tempdir())
}
#> Running meta-analysis (random_effects) on 4 studies...
#> Report written to: /tmp/RtmpxsxSbD/metaXpress_report.html
# }