generate_garnett_marker_file: Generate a Garnett marker file from top_markers output.

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Generate a Garnett marker file from top_markers output.

Description

Generate a Garnett marker file from top_markers output.

Usage

generate_garnett_marker_file(
  marker_test_res,
  file = "./marker_file.txt",
  max_genes_per_group = 10,
  remove_duplicate_genes = FALSE
)

Arguments

marker_test_res	Tibble of top markers, output of top_markers.
file	Path to the marker file to be generated. Default is "./marker_file.txt".
max_genes_per_group	Numeric, the maximum number of genes to output per cell type entry. Default is 10.
remove_duplicate_genes	Logical indicating whether marker genes that mark multiple cell groups should be excluded. Default is FALSE. When FALSE, a message will be emitted when duplicates are present.

Value

None, marker file is written to file parameter location.

cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.