Retrieving specific portions of the Immune Receptor beyond the junction (or CDR3). about scirpy

[grst]

Hi,

with the ir.get.airr you can query any field specified in the AIRR Rearrangement standard as long as it is read in.

So in your case, it would be

ir.get.airr(
    adata,
   "cdr1_aa", # field name according to Rearrangement standard
   "VJ_1" # VJ_1 refers to the primary alpha/gamma/light chain, see https://scirpy.scverse.org/en/latest/ir-biology.html#dual-tcrs-and-allelically-included-b-cells
)

[ivandatasci]

Hi Gregor.

That is exactly what I was asking about. Thank you.

For posterity, beyond locus and cdr1, a complete list of IR properties contained in your MuData object can be displayed like this:

>>> mdata['airr'].obsm['airr']

[[{c_call: 'IGHG', cdr1: 'GGATTCTCCCTCAATAATAAGTAC', cdr1_aa: ..., ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGAGCATTGGTATTAGATTAGCC', ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGTCCAGTGAGAGCGTTTATAATAACAACTACTTATCC', ...}],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGAACATTGGTAGTAATTTGGCC', ...}],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGAGCATTGGTAGTAGCTTAGCC', ...}],
 [{c_call: 'IGHG', cdr1: 'GGATTCTCCTTCAGTAGCGGCTAC', cdr1_aa: ..., ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTGAGGATATTAATAACTACTTATCC', ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTGAGGATATTAGTGGTAGATTAGGC', ...}],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGAGCATTGGTAGTAGCTTAGCC', ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGACCATTAGCAGTTGGTTATCC', ...}, ...],
 ...,
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGACCATTAGTAGCTACTTAGCC', ...}],
 [{c_call: 'IGHG', cdr1: 'GGATTCTCCTTCAATAATCTC', cdr1_aa: 'GFSFNNL', ...}],
 [{c_call: 'IGHG', cdr1: 'GGATTCTCCTTCAGTAGCAGCTTC', cdr1_aa: ..., ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGGATATTGCTAGTAGCTACTTAGCCTGG', ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTGAGAGCATTGGTGATCACTTATCC', ...}],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTGAAAGCATTAGCAACTACTTATCC', ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGAGCATTAGGAGTTGGTTAGCC', ...}],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGAGCATTAGTAGTTACTTATCC', ...}, ...],
 [{c_call: 'IGKC1', cdr1: 'CAGGCCAGTCAGAGCATTAGTAGCTACTTATCC', ...}, ...]]
--------------------------------------------------------------------------------
type: 1520 * var * {
    c_call: ?string,
    cdr1: ?string,
    cdr1_aa: ?string,
    cdr2: string,
    cdr2_aa: string,
    cdr3: ?string,
    cdr3_aa: ?string,
    consensus_count: int64,
    d_call: ?string,
    d_cigar: ?unknown,
    duplicate_count: int64,
    fwr1: string,
    fwr1_aa: string,
    fwr2: string,
    fwr2_aa: string,
    fwr3: string,
    fwr3_aa: string,
    fwr4: string,
    fwr4_aa: string,
    germline_alignment: ?unknown,
    high_confidence: bool,
    is_cell: bool,
    j_call: string,
    j_cigar: ?unknown,
    junction: string,
    junction_aa: string,
    locus: string,
    productive: bool,
    rev_comp: ?unknown,
    sequence: ?unknown,
    sequence_alignment: ?unknown,
    sequence_id: ?unknown,
    v_call: string,
    v_cigar: ?unknown
}

I hope the community finds this information useful.

Ivan