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 (
Union
[str
,Path
]) – Path tofilterd_contig_annotations.csv
,all_contig_annotations.csv
orall_contig_annotations.json
.filtered (
bool
(default:True
)) – Only keep filtered contig annotations (i.e.is_cell
andhigh_confidence
). If usingfiltered_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:
- Returns:
AnnData object with AIRR data in
obsm["airr"]
for each cell. For more details see Storing AIRR rearrangement data in AnnData.