getComplexity

Calculate the complexity of expression data, determining the number of features (genes) required to reach half of the total expression sum in a dataset.

Usage

getComplexity(
  seu_obj = NULL,
  features = NULL,
  expMat = "path_to_expMat",
  platform = NULL
)

Arguments

seu_obj

An optional Seurat object containing the expression data. If provided, the function will calculate complexity based on the data in the object.

features

Optional character vector of features to focus the complexity calculation on a subset of all features. If NULL, all features are considered.

expMat

The path to the expression matrix file or directory containing expression data files. This parameter is used if no Seurat object is provided. This function supports processing of '.mtx.gz' for sparse matrices, or '.h5' files for HDF5 format expression matrices.

platform

The platform from which the data originates. Valid options are 'Xenium', 'CosMx', and 'Merscope'.

Details

Calculate the total expression and determines the minimal set of features accounting for at least half of this total, either across all features or a specified subset. If a Seurat object is used, it derives the complexity from the RNA assay counts.