simba.pp.select_variable_genes
- simba.pp.select_variable_genes(adata, layer='raw', span=0.3, n_top_genes=2000)[source]
Select highly variable genes.
This function implenments the method ‘vst’ in Seurat v3. Inspired by Scanpy.
- Parameters:
adata (AnnData) – Annotated data matrix.
layer (str, optional (default: ‘raw’)) – The layer to use for calculating variable genes.
span (float, optional (default: 0.3)) – Loess smoothing factor
n_top_genes (int, optional (default: 2000)) – The number of genes to keep
- Returns:
updates adata with the following fields.
variances_norm (float, (adata.var[‘variances_norm’])) – Normalized variance per gene
variances (float, (adata.var[‘variances’])) – Variance per gene.
means (float, (adata.var[‘means’])) – Means per gene
highly_variable (bool (adata.var[‘highly_variable’])) – Indicator of variable genes