snapatac2.pp.add_frip#
- snapatac2.pp.add_frip(adata, regions, *, inplace=True, n_jobs=8)[source]#
Add fraction of reads in peaks (FRiP) to the AnnData object.
- Parameters:
adata (
AnnData|list[AnnData]) – The (annotated) data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to regions. adata could also be a list of AnnData objects. In this case, the function will be applied to each AnnData object in parallel.regions (
dict[str,Path|list[str]]) – A dictionary containing the peak sets to compute FRiP. The keys are peak set names and the values are either a bed file name or a list of strings representing genomic regions. For example, {“promoter_frac”: “promoter.bed”, “enhancer_frac”: [“chr1:100-200”, “chr2:300-400”]}.inplace (
bool) – Whether to add the results to adata.obs or return it as a dictionary.n_jobs (
int) – Number of jobs to run in parallel when adata is a list. If n_jobs=-1, all CPUs will be used.
- Return type:
UnionType[dict[str,list[float]],list[dict[str,list[float]]],None]