multivelovae.aggregate_peaks_10x

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

Aggregate promoter and enhancer peaks to genes based on the 10X linkage file.

Args:

adata_atac (anndata.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, optional):

Maximum distance for peaks to be included for a gene. Defaults to 10000.

min_corr (float, optional):

Minimum correlation for a peak to be considered as enhancer. Defaults to 0.5.

gene_body (bool, optional):

Whether to add gene body peaks to the associated promoters. Defaults to False.

return_dict (bool, optional):

Whether to return promoter and enhancer dictionaries. Defaults to False.

verbose (bool, optional):

Whether to print number of genes with promoter peaks. Defaults to False.

Returns:

Tuple(anndata.AnnData, dict, dict):

if return_dict:

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

• A dictionary which stores genes and promoter peaks.

• A dictionary which stores genes and enhancer peaks.

anndata.AnnData:

if not return dict: A new ATAC anndata object which stores gene aggreagted peak counts.