pp
filter_genes(adata, min_cutoff=0.01, max_cutoff=1, expression_cutoff_99q=0, layer=None)
Similar function to sc.pp.filter_genes but uses percentage instead of counts.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
adata |
_type_
|
Anndata |
required |
min_cutoff |
float
|
Minimum percentage of counts required for a gene to pass filtering. Defaults to 0.01. |
0.01
|
max_cutoff |
int
|
Maximum percentage of counts required for a gene to pass filtering. Defaults to 0.01.. Defaults to 1. |
1
|
expression_cutoff_99q |
int
|
Minimum expression level of gene at 99th percentile. Defaults to 0. |
0
|
batch_highly_variable_genes(adata, batch_key, n_top_genes, layer=None, subset=False)
Similar function to sc.pp.highly_variable_genes but fixes what I think its a bug in the implementation. Uses flavor seurat_v3 only.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
adata |
_type_
|
Anndata object |
required |
batch_key |
_type_
|
Batch key |
required |
n_top_genes |
_type_
|
description |
required |
layer |
_type_
|
description. Defaults to None. |
None
|
subset |
bool
|
description. Defaults to False. |
False
|