calculate_expression: Counts average expression of gene set (Use in package)

In SlimR: Machine Learning-Assisted, Marker-Based Tool for Single-Cell and Spatial Transcriptomics Annotation

Counts average expression of gene set (Use in package)

Description

Counts average expression of gene set (Use in package)

Usage

calculate_expression(
  object,
  features,
  assay = NULL,
  cluster_col = NULL,
  colour_low = "white",
  colour_high = "navy"
)

Arguments

object	Enter a Seurat object.
features	Enter one or a set of markers.
assay	Enter the assay used by the Seurat object, such as "RNA". Default parameters use "assay = NULL".
cluster_col	Enter the meta.data column in the Seurat object to be annotated, such as "seurat_cluster". Default parameters use "cluster_col = NULL".
colour_low	Color for lowest expression level. (default = "white")
colour_high	Color for highest expression level. (default = "black")

Value

Average expression genes and relatied informations in the input "Seurat" object given "cluster_col" and given "features".

See Also

Other Section_1_Functions_Use_in_Package: calculate_cluster_variability(), calculate_expression_skewness(), calculate_probability(), estimate_batch_effect(), extract_dataset_features(), generate_training_data(), postprocess_parameters(), predict_optimal_parameters(), train_parameter_model()

SlimR documentation built on Dec. 17, 2025, 5:09 p.m.