multivelo.aggregate_peaks_10x

multivelo.aggregate_peaks_10x(adata_atac, peak_annot_file, linkage_file, peak_dist=10000, min_corr=0.5, gene_body=False, return_dict=False, verbose=False)

Peak to gene aggregation.

This function aggregates promoter and enhancer peaks to genes based on the 10X linkage file.

Parameters:

  • adata_atac (AnnData) – ATAC anndata object which stores raw peak counts.

  • peak_annot_file (str) – Peak annotation file from 10X CellRanger ARC.

  • linkage_file (str) – Peak-gene linkage file from 10X CellRanger ARC. This file stores highly correlated peak-peak and peak-gene pair information.

  • peak_dist (int (default: 10000)) – Maximum distance for peaks to be included for a gene.

  • min_corr (float (default: 0.5)) – Minimum correlation for a peak to be considered as enhancer.

  • gene_body (bool (default: False)) – Whether to add gene body peaks to the associated promoters.

  • return_dict (bool (default: False)) – Whether to return promoter and enhancer dictionaries.

  • verbose (bool (default: False)) – Whether to print number of genes with promoter peaks.

Returns:

  • A new ATAC anndata object which stores gene aggreagted peak counts.

  • Additionally, if return_dict==True – A dictionary which stores genes and promoter peaks. And a dictionary which stores genes and enhancer peaks.