episcanpy.api.tl.geneactivity

episcanpy.api.tl.geneactivity(adata, gtf_file, key_added='gene', upstream=5000, feature_type='gene', annotation='HAVANA', layer_name='geneactivity', raw=False, copy=True)

Build an AnnData object containing the number of open features (windows, peaks, etc) overlapping genes (gene bodies + 5kb upstream of the TSS). It is possible to extend the distance from the TSS with the upstream parameter.

Rather than using multiple time the same gene, it is possible to specify which genome annotation is desired using the parameter annotation. as the GTF files can often contain multiple annotations for genes (HAVANA, ENSEMBL, etc.).

Alternatively, if you want to obtain the gene activity at something else than genes, like transcipts. It is possible as well. The feature_type can be specified.

TSS = Transcription Starting Site

adata : input AnnData gtf_file : input gtf file name + path key_added : to save the geneactivity matrix as an adata.uns object if upstream : featyre_type : transcripts or genes annotation : layer_name : raw : copy :