scirpy.io.read_10x_vdj

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scirpy.io.read_10x_vdj#

scirpy.io.read_10x_vdj(path, filtered=True, include_fields=None, **kwargs)#

Read AIRR data from 10x Genomics cell-ranger output.

Supports all_contig_annotations.json and {all,filtered}_contig_annotations.csv.

If the json file is available, it is preferable as it contains additional information about V(D)J-junction insertions. Other than that there should be no difference.

Note

Since scirpy v0.13, there are no restrictions on the AIRR data that can be stored in the scirpy data structure, except that each receptor chain needs to be associated with a cell.

The scirpy Immune receptor (IR) model is now applied in later step using the index_chains() function.

For more information, see Storing AIRR rearrangement data in AnnData.

Parameters:

  • path (str | Path) – Path to filterd_contig_annotations.csv, all_contig_annotations.csv or all_contig_annotations.json.

  • filtered (bool (default: True)) – Only keep filtered contig annotations (i.e. is_cell and high_confidence). If using filtered_contig_annotations.csv already, this option is futile.

  • include_fields (Optional[Any] (default: None)) – Deprecated. Does not have any effect as of v0.13.

  • **kwargs – are passed to from_airr_cells().

Return type:

AnnData

Returns:

AnnData object with AIRR data in obsm["airr"] for each cell. For more details see Storing AIRR rearrangement data in AnnData.

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