generate_pdf_report: Create the Quality Control report

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Create the Quality Control report

Description

Normally used as part of the analysis_quickstart() function, refer to its implementation for example code.

Usage

generate_pdf_report(
  dataset,
  output_dir,
  norm_algorithm = "vwmb",
  rollup_algorithm = "maxlfq",
  pca_sample_labels = "auto",
  var_explained_sample_metadata = NULL
)

Arguments

dataset	your dataset
output_dir	output directory where all output files are stored, must be an existing directory
norm_algorithm	normalization algorithm(s). See analysis_quickstart function documentation
rollup_algorithm	peptide-to-protein rollup strategy. See analysis_quickstart function documentation
pca_sample_labels	configuration for PCA plot labels. See analysis_quickstart function documentation
var_explained_sample_metadata	configuration for variance-explained analyses. See analysis_quickstart function documentation

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.