stereo.core.StPipeline.filter_genes#
- StPipeline.filter_genes(min_cell=None, max_cell=None, gene_list=None, mean_umi_gt=None, filter_raw=True, inplace=True)[source]#
Filter genes based on the numbers of cells or counts.
- Parameters:
min_cell (
Optional
[int
]) – minimum number of cells expressed required for a gene to pass filering.max_cell (
Optional
[int
]) – maximum number of cells expressed required for a gene to pass filering.gene_list (
Union
[ndarray
,list
,None
]) – the list of genes to be retained.mean_umi_gt (
Optional
[float
]) – genes mean umi should greater than this.filter_raw (
Optional
[bool
]) – whether to filter raw data meanwhile.inplace (
bool
) – whether to inplace the previous data or return a new data.
- Returns:
An object of StereoExpData.
Depending on
inplace
, ifTrue
, the data will be replaced by those filtered.