mtopic.pp.filter_var_list

mtopic.pp.filter_var_list(path, var)

Retain a specific list of features in a MuData object.

This function retains only the specified list of features (e.g., genes, proteins) in a MuData object and removes all other features. It is designed to streamline downstream analysis by focusing on a predefined subset of relevant features.

Parameters:

• path (str) – The file path to the .h5mu file containing the MuData object to be processed.

• var (list of str) – A list of feature names to be retained in the MuData object.

Returns:

A MuData object containing only the specified features.

Return type:

muon.MuData

Example:

import mtopic

# Load MuData object and specify features to retain
path = "path/to/file.h5mu"
features_to_keep = ['gene1', 'gene2', 'gene3']

# Retain specified features
filtered_mdata = mtopic.pp.filter_var_list(path, var=features_to_keep)

Notes:

• The function loads the MuData object from the specified path using mtopic.read.h5mu and retains only the features specified in the var list using mu.pp.filter_var.

• After filtering, the mdata.update() method ensures consistency across the multimodal data structure.

• Ensure the feature names in var match the names in the dataset to avoid errors.