report_de: Generate a report for differential expression analysis

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Generate a report for differential expression analysis

Description

Generate a report for differential expression analysis

Usage

report_de(
  res,
  logFC_threshold = 0.25,
  padj_cutoff = 0.05,
  n_label = 5,
  report_folder_path = getwd(),
  report_file = "de_report_scflow"
)

Arguments

res	Differential expression result table from perform_de() function.
logFC_threshold	fold change up/down threshold.
padj_cutoff	the adjusted pvalue cutoff threshold.
n_label	number of genes to be labelled in the volcano plot.
report_folder_path	folder path to save the report.
report_file	filename for report (without an extension).

See Also

Other differential gene expression: .filter_sce_genes_for_de(), .generate_model_from_vars(), .perform_de_with_mast(), .preprocess_sce_for_de(), perform_de(), pseudobulk_sce(), volcano_plot()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.