Accessing Monoclonal Antibody Data

Workflow overview

The workflow for getting mAb data is very similar to getting study data or groups. Pass the availableMabs object to the getMabs method. This can be filtered in a pipe as shown below.

con <- connectDS()

pgt121 <- con$availableMabs[mab_name_std == "PGT121"] |>
  con$getMabs()

For the new mAb object, datsets are loaded automatically.

pgt121$datasets |>
  names()
#> [1] "NABMAb" "PKMAb"

And each dataset can be accessed in the same fashion as accessing an item in a named list.

pgt121$datasets$NABMAb

View metadata concerning the mAb object

Each mab object has metadata associated with it that can be viewed.

pgt121$mabMetadata
#> Key: <mab_id>
#>        mab_id mab_name_std mab_lanl_id mab_hxb2_location mab_ab_binding_type mab_isotype mab_class_id assays_available
#>        <char>       <char>      <char>            <char>              <char>      <char>       <char>           <char>
#> 1: cds_mab_26       PGT121        2635               Env     glycan/gp120 V3         IgG         <NA>  NAB MAB, PK MAB
#>                         studies_available     donor_id sequences_available
#>                                    <char>       <char>              <lgcl>
#> 1: cvd270, cvd471, cvd473, cvd554, cvd719 cds_donor_36                TRUE
pgt121$donorMetadata
#>        donor_id donor_lanl_id donor_code donor_species donor_clade lineage_sequences_available mab_count sequence_count
#>          <char>        <char>     <char>        <char>      <char>                      <lgcl>     <int>          <int>
#> 1: cds_donor_36            26   Donor 17         human           A                       FALSE         8              8
pgt121$mabMixMetadata
#> Key: <mab_mix_id>
#>          mab_mix_id            mab_mix_name_std mab_mix_name_other mab_mix_type virus_count titer_50_geomean
#>              <char>                      <char>             <char>       <char>       <int>            <num>
#>  1:  cds_mab_mix_36                      PGT121                      Single mAb         539       0.07817056
#>  2: cds_mab_mix_459       PGT121 (Clinical BDS)             PGT121   Single mAb          36       0.09557637
#>  3: cds_mab_mix_460           PGT121 (Catalant)             PGT121   Single mAb          35       0.09651576
#>  4: cds_mab_mix_461 PGT121 (Reference Standard)             PGT121   Single mAb           8       0.06997322
#>  5: cds_mab_mix_476 PGT121 (Reference Standard)             PGT121   Single mAb          NA               NA
#>  6: cds_mab_mix_477     PGT121 (STAB147.Tox 22)             PGT121   Single mAb           7       0.06212521
#>  7: cds_mab_mix_478     PGT121 (STAB150.GMP 20)             PGT121   Single mAb           7       0.07924972
#>  8: cds_mab_mix_479     PGT121 (STAB154.GMP 10)             PGT121   Single mAb           7       0.06973818
#>  9: cds_mab_mix_588     PGT121 Parental (MS-42)             PGT121   Single mAb          NA               NA
#> 10: cds_mab_mix_589      PGT121 variant (MS-43)             PGT121   Single mAb          NA               NA
#> 11: cds_mab_mix_590     PGT121 variant (MS-414)             PGT121   Single mAb          NA               NA
#> 12: cds_mab_mix_591     PGT121 variant (MS-444)             PGT121   Single mAb          NA               NA
#> 13:  cds_mab_mix_67           PGT121 + PGDM1400                     MAb mixture         293       0.01915122
#> 14:  cds_mab_mix_68             PGT121 + PGT145                     MAb mixture         293       0.06146521