calculate_qc_metrics
Calculate quality control metrics for AnnData, including total counts, gene numbers, and percentages of ribosomal and mitochondrial counts, to evaluate single-cell RNA sequencing data.
Instructions
Calculate quality control metrics(common metrics: total counts, gene number, percentage of counts in ribosomal and mitochondrial) for AnnData.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| expr_type | No | Name of kind of values in X. | counts |
| layer | No | If provided, use adata.layers[layer] for expression values instead of adata.X | |
| log1p | No | Set to False to skip computing log1p transformed annotations. | |
| percent_top | No | List of ranks (where genes are ranked by expression) at which the cumulative proportion of expression will be reported as a percentage. | |
| qc_vars | No | Keys for boolean columns of .var which identify variables you could want to control for mark_var tool should be called frist when you want to calculate mt, ribo, hb, and check tool output for var columns | |
| use_raw | No | If True, use adata.raw.X for expression values instead of adata.X | |
| var_type | No | The kind of thing the variables are. | genes |