pegasus.identify_robust_genes¶
- pegasus.identify_robust_genes(data, percent_cells=0.05)[source]¶
Identify robust genes as candidates for HVG selection and remove genes that are not expressed in any cells.
- Parameters
data (
pegasusio.MultimodalData
) – Use current selected modality in data, which should contain one RNA expression matrix.percent_cells (
float
, optional, default:0.05
) – Only assign genes to berobust
that are expressed in at leastpercent_cells
% of cells.
- Return type
None
- Returns
None
Update
data.var
–n_cells
: Total number of cells in which each gene is measured.percent_cells
: Percent of cells in which each gene is measured.robust
: Boolean type indicating if a gene is robust based on the QC metrics.highly_variable_features
: Boolean type indicating if a gene is a highly variable feature. By default, set all robust genes as highly variable features.
Examples
>>> pg.identify_robust_genes(data, percent_cells = 0.05)