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 be robust that are expressed in at least percent_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)