Distances without cdr3_a_nucseq and cdr3_b_nucseq

[andreas-wilm]

Hi Koshlan,

According to the documentation on input requirements, one or more of the following columns are required and are case-sensitive:

    ‘v_a_gene’, ‘v_b_gene’, ‘v_g_gene’, or ‘v_d_gene’
    ‘j_a_gene’, ‘j_b_gene’, ‘j_g_gene’, or ‘j_d_gene’
    ‘cdr3_a_aa’, ‘cdr3_b_aa’, ‘cdr3_g_aa’, or ‘cdr3a_d_aa’
    ‘cdr3_a_nucseq’, ‘cdr3_b_nucseq, ‘cdr3_g_nucseq’, or ‘cdr3a_d_nucseq’

However, I've used TCRdist3 to compute distances on dataframes without cdr3_a_nucseq and cdr3_b_nucseq, which seems to have worked fine, but am now wondering whether it did the right thing.

Apologies for the paranoid question, Andreas

[kmayerb]

• The nucleotide information is not needed to compute a TCRdist.
• However, if you don't include cdr3_[abdg]_nucseq, then any set of clones with identical v and j genes and identical cdr3_baa (amino acid level identical) will be grouped together. You may or may not want this, but if you want to track clones unique at the nucleotide level cdr3[abdg]_nucseq would be required. At this point you're a bit of a power user so you may be tracking unique clones with another column. For more details: https://tcrdist3.readthedocs.io/en/latest/inputs.html#critical-information

Tcrdist3 only requires 3 input columns for single chain analysis (i.e., for beta chain cdr3_b_aa and v_b_gene, j_b_gene) and 6 columns for paired chain analysis (i.e., cdr3_b_aa, v_b_gene, j_b_gene, cdr3_a_aa, v_a_gene, and j_a_gene). More columns can be included depending on the application.

[andreas-wilm]

Thank you. That makes sense. It might be useful to add this to https://tcrdist3.readthedocs.io/en/latest/inputs.html which currently lists the nucseqs as requirement (under "One or more of the following columns are required and are case-sensitive"). Best

[kmayerb]

Done. Thanks.

On Thu, Nov 4, 2021 at 7:29 PM Andreas Wilm @.***> wrote:

Thank you. That makes sense. It might be useful to add this to https://tcrdist3.readthedocs.io/en/latest/inputs.html which currently lists the nucseqs as requirement. Best

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