scdynomics.utils.pp.qc
For filtering low quality cells
author: jy
Functions
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Two QC filters to pre-process the multimodal adata. |
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QC with controling on n_genes and mt genes. |
- scdynomics.utils.pp.qc.filter_multimodal_adata(adata: anndata.AnnData, layers: list = [None], min_genes: int = 200, min_cells: int = None, percent_top: int = 20, remove_outliers: bool = True, log1p: bool = True, remove_mono: bool = False) anndata.AnnData
Two QC filters to pre-process the multimodal adata.
- Parameters:
- adata:
ad.AnnData The multimodal annotated data matrix to be filtered.
- layers:
list(default:[None]) List of layers in the AnnData object corresponding to different modalities.
- min_genes:
int(default:200) Minimum number of genes expressed required for a cell to pass filtering per modality.
- min_cells:
int(default:None) Minimum number of cells required for a gene to be retained.
- percent_top:
int(default:20) Proportions of counts in top-expressed genes to calculate.
- remove_outliers:
bool(default:True) If True, removes identified outlier cells based on MADs.
- log1p:
bool(default:True) If True, computes log1p transformed metrics.
- remove_mono:
bool(default:False) If True, removes cells that only express data in a single modality.
- adata:
- Returns:
ad.AnnData The filtered multimodal AnnData object.
- scdynomics.utils.pp.qc.qc_metrics(adata: anndata.AnnData = None, min_genes: int = 200, percent_top: int = 20, remove_outliers: bool = True, log1p: bool = True) anndata.AnnData
QC with controling on n_genes and mt genes.
Refering to: sc-best-practices.org/preprocessing_visualization/quality_control.html
- Parameters:
- adata:
ad.AnnData(default:None) The annotated data matrix to be filtered.
- min_genes:
int(default:200) Minimum number of genes expressed required for a cell to pass filtering.
- percent_top:
int(default:20) Proportions of counts in top-expressed genes to calculate as a QC metric.
- remove_outliers:
bool(default:True) If True, removes identified outlier cells based on median absolute deviation (MAD).
- log1p:
bool(default:True) If True, computes log1p transformed metrics during the QC process.
- adata:
- Returns:
ad.AnnData The quality-controlled AnnData object.