scirpy.io.IrChain¶
-
class
scirpy.io.IrChain(locus, *, cdr3=None, cdr3_nt=None, expr=None, expr_raw=None, is_productive=None, v_gene=None, d_gene=None, j_gene=None, c_gene=None, junction_ins=None)¶ Data structure for an immune cell receptor chain.
- Parameters
- locus : {‘TRA’, ‘TRG’, ‘IGK’, ‘IGL’, ‘TRB’, ‘TRD’, ‘IGH’, ‘other’}
Literal[‘TRA’, ‘TRG’, ‘IGK’, ‘IGL’, ‘TRB’, ‘TRD’, ‘IGH’, ‘other’] IGMT locus name or “other”. See https://docs.airr-community.org/en/latest/datarep/rearrangements.html#locus-names.
- cdr3 :
str,NoneOptional[str] (default:None) Amino acid sequence of the CDR3 region
- cdr3_nt :
str,NoneOptional[str] (default:None) Nucleotide sequence fo the CDR3 region
- expr :
float,NoneOptional[float] (default:None) Normalized read count for the CDR3 region. Will be UMIs for 10x and TPM for SmartSeq2.
- expr_raw :
float,NoneOptional[float] (default:None) Raw read count for the CDR3 regions.
- is_productive :
bool,NoneOptional[bool] (default:None) Is the chain productive?
- v_gene :
str,NoneOptional[str] (default:None) gene symbol of v gene
- d_gene :
str,NoneOptional[str] (default:None) gene symbol of d gene
- j_gene :
str,NoneOptional[str] (default:None) gene symbol of j gene
- c_gene :
str,NoneOptional[str] (default:None) gene symbol of c gene
- junction_ins :
int,NoneOptional[int] (default:None) nucleotides inserted in the junctions. For VJ chains: nucleotides inserted in the VJ junction For VDJ chains: sum of nucleotides inserted in the VD + DJ junction
- locus : {‘TRA’, ‘TRG’, ‘IGK’, ‘IGL’, ‘TRB’, ‘TRD’, ‘IGH’, ‘other’}
Attributes
Valid chains are IMGT locus names or “other” see https://docs.airr-community.org/en/latest/datarep/rearrangements.html#locus-names
Chains with the V-D-J junction
Chains with the V-J junction
Methods