pegasus.qc_metrics¶
-
pegasus.
qc_metrics
(data, mito_prefix='MT-', min_genes=500, max_genes=6000, min_umis=100, max_umis=600000, percent_mito=10.0, percent_cells=0.05)[source]¶ Generate Quality Control (QC) metrics on the dataset.
- Parameters
data (
anndata.AnnData
) – Annotated data matrix with rows for cells and columns for genes.mito_prefix (
str
, optional, default:"MT-"
) – Prefix for mitochondrial genes.min_genes (
int
, optional, default:500
) – Only keep cells with at leastmin_genes
genes.max_genes (
int
, optional, default:6000
) – Only keep cells with less thanmax_genes
genes.min_umis (
int
, optional, default:100
) – Only keep cells with at leastmin_umis
UMIs.max_umis (
int
, optional, default:600,000
) – Only keep cells with less thanmax_umis
UMIs.percent_mito (
float
, optional, default:10.0
) – Only keep cells with percent mitochondrial genes less thanpercent_mito
% of total counts.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.obs
–n_genes
: Total number of genes for each cell.n_counts
: Total number of counts for each cell.percent_mito
: Percent of mitochondrial genes for each cell.passed_qc
: Boolean type indicating if a cell passes the QC process based on the QC metrics.
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.qcmetrics(adata)