scgenome.tl.aggregate_genes

scgenome.tl.aggregate_genes(adata, genes, agg_layers=None, agg_var=None)

Aggregate copy number by gene to create gene CN matrix

Currently only does segment width weighted mean aggregation.

Parameters:

• adata (AnnData) – copy number data

• genes (PyRanges) – gene data

• agg_layers (List, optional) – list of layers to aggregate, by default None, all layers

• agg_var (List, optional) – list of obs columns to aggregate, by default None, all columns

• cluster_col (str, optional) – column with cluster ids, by default ‘cluster_id’

Returns:

aggregated gene copy number

Return type:

AnnData