scirpy.io.read_10x_vdj

scirpy.io.read_10x_vdj(path, filtered=True)

Read IR 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

Reading data into Scirpy has the following constraints:

  • Each cell can have up to four productive chains chains (Dual IR): two VJ and two VDJ chains.

  • Excess chains are ignored (those with lowest read count/UMI count) and cells flagged as Multichain-cell.

  • Non-productive chains are ignored.

  • Chain loci must be valid IGMT locus names.

  • Excess chains, non-productive chains, chains without a CDR3 sequence, or chains with invalid loci are serialized to JSON and stored in the extra_chains column. They are not used by scirpy except when exporting the AnnData object to AIRR format.

For more information, see Immune receptor (IR) model.

Parameters
path : str | PathUnion[str, Path]

Path to filterd_contig_annotations.csv, all_contig_annotations.csv or all_contig_annotations.json.

filtered : boolbool (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.

Return type

AnnDataAnnData

Returns

AnnData object with IR data in obs for each cell. For more details see Data structure.