dynamo.pp.filter_genes_by_clusters
- dynamo.pp.filter_genes_by_clusters(adata, cluster, min_avg_U=0.02, min_avg_S=0.08, size_limit=40)[source]
Prepare filtering genes on the basis of cluster-wise expression threshold.
This function is taken from velocyto in order to reproduce velocyto’s DentateGyrus notebook.
- Parameters:
adata (
AnnData) – an Anndata object.cluster (
str) – a column name in the adata.obs attribute which will be used for cluster specific expression filtering.min_avg_U (
float) – include genes that have unspliced average bigger than min_avg_U in at least one of the clusters. Defaults to 0.02.min_avg_S (
float) – include genes that have spliced average bigger than min_avg_U in at least one of the clusters. Defaults to 0.08.size_limit (
int) – the max number of members to be considered in a cluster during calculation. Defaults to 40.
- Return type:
- Returns:
A boolean array corresponding to genes selected.