scRepertoire - combineTCR error

Question

[sudeshna]

Hello,

I am currently using the package scRepertoire for single-cell TCR and BCR repertoire analysis. I have 4 filtered_contig_annotations.csv TCR files obtained from the 10X Genomics Cell Ranger 5.0.0 pipeline and as mentioned in the scRepertoire vignette, I have created the object tcr_list. However, when I call combineTCR, I get the following error

combine_tcr<-combineTCR(tcr_list,samples=c("Control","Control","Patient","Patient"),
                    ID=c("T1","T2","T1","T2") ,cells="T-AB")

Error in `$<-.data.frame`(`*tmp*`, "sample", value = "Control"): replacement has 1 row, data has 0

The tcr_list object looks like this-

str(tcr_list)

List of 4
 $ :'data.frame':   3528 obs. of  18 variables:
  ..$ barcode         : chr [1:3528] "AAACCTGAGCTTCGCG-1" "AAACCTGAGCTTCGCG-1" "AAACCTGAGTCTCGGC-1" "AAACCTGAGTCTCGGC-1" ...
  ..$ is_cell         : chr [1:3528] "true" "true" "true" "true" ...
  ..$ contig_id       : chr [1:3528] "AAACCTGAGCTTCGCG-1_contig_1" "AAACCTGAGCTTCGCG-1_contig_2" "AAACCTGAGTCTCGGC-1_contig_1" "AAACCTGAGTCTCGGC-1_contig_2" ...
  ..$ high_confidence : chr [1:3528] "true" "true" "true" "true" ...
  ..$ length          : int [1:3528] 492 471 484 574 496 486 499 646 465 496 ...
  ..$ chain           : chr [1:3528] "TRB" "TRA" "TRB" "TRA" ...
  ..$ v_gene          : chr [1:3528] "TRBV27" "TRAV13-1" "TRBV4-2" "TRAV19" ...
  ..$ d_gene          : chr [1:3528] "" "" "TRBD2" "" ...
  ..$ j_gene          : chr [1:3528] "TRBJ1-5" "TRAJ52" "TRBJ2-1" "TRAJ45" ...
  ..$ c_gene          : chr [1:3528] "TRBC1" "TRAC" "TRBC2" "TRAC" ...
  ..$ full_length     : chr [1:3528] "true" "true" "true" "true" ...
  ..$ productive      : chr [1:3528] "true" "true" "true" "true" ...
  ..$ cdr3            : chr [1:3528] "CASSLVPNHQPQHF" "CAASIGAGGTSYGKLTF" "CASSHGTSGTYNEQFF" "CALSEWYSGGGADGLTF" ...
  ..$ cdr3_nt         : chr [1:3528] "TGTGCCAGCAGTTTAGTGCCCAATCATCAGCCCCAGCATTTT" "TGTGCAGCAAGTATAGGAGCTGGTGGTACTAGCTATGGAAAGCTGACATTT" "TGTGCCAGCAGCCACGGGACTAGCGGGACCTACAATGAGCAGTTCTTC" "TGTGCTCTGAGTGAGTGGTATTCAGGAGGAGGTGCTGACGGACTCACCTTT" ...
  ..$ reads           : int [1:3528] 4640 4362 3889 1027 4755 3193 17028 2292 1076 7997 ...
  ..$ umis            : int [1:3528] 7 8 5 2 12 6 32 4 3 20 ...
  ..$ raw_clonotype_id: chr [1:3528] "clonotype339" "clonotype339" "clonotype6" "clonotype6" ...
  ..$ raw_consensus_id: chr [1:3528] "clonotype339_consensus_1" "clonotype339_consensus_2" "clonotype6_consensus_1" "clonotype6_consensus_2" ...
 $ :'data.frame':   3823 obs. of  18 variables:
  ..$ barcode         : chr [1:3823] "AAACCTGAGACAGGCT-1" "AAACCTGAGACAGGCT-1" "AAACCTGAGTGTACCT-1" "AAACCTGAGTGTACCT-1" ...
  ..$ is_cell         : chr [1:3823] "true" "true" "true" "true" ...
  ..$ contig_id       : chr [1:3823] "AAACCTGAGACAGGCT-1_contig_1" "AAACCTGAGACAGGCT-1_contig_2" "AAACCTGAGTGTACCT-1_contig_1" "AAACCTGAGTGTACCT-1_contig_2" ...
  ..$ high_confidence : chr [1:3823] "true" "true" "true" "true" ...
  ..$ length          : int [1:3823] 503 610 491 492 522 520 549 623 513 501 ...
  ..$ chain           : chr [1:3823] "TRB" "TRA" "TRA" "TRB" ...
  ..$ v_gene          : chr [1:3823] "TRBV5-1" "TRAV8-6" "TRAV24" "TRBV27" ...
  ..$ d_gene          : chr [1:3823] "" "" "" "TRBD1" ...
  ..$ j_gene          : chr [1:3823] "TRBJ1-5" "TRAJ15" "TRAJ47" "TRBJ2-7" ...
  ..$ c_gene          : chr [1:3823] "TRBC1" "TRAC" "TRAC" "TRBC2" ...
  ..$ full_length     : chr [1:3823] "true" "true" "true" "true" ...
  ..$ productive      : chr [1:3823] "true" "true" "true" "true" ...
  ..$ cdr3            : chr [1:3823] "CASSLGSGINQPQHF" "CAVSFNQAGTALIF" "CASPMEYGNKLVF" "CASSLWTGAHEQYF" ...
  ..$ cdr3_nt         : chr [1:3823] "TGCGCCAGCAGCCTCGGCTCAGGAATCAATCAGCCCCAGCATTTT" "TGTGCTGTGAGTTTCAACCAGGCAGGAACTGCTCTGATCTTT" "TGTGCCTCCCCCATGGAATATGGAAACAAGCTGGTCTTT" "TGTGCCAGCAGTTTATGGACAGGGGCCCACGAGCAGTACTTC" ...
  ..$ reads           : int [1:3823] 9902 1551 1408 1710 692 2377 3960 5885 1440 497 ...
  ..$ umis            : int [1:3823] 20 4 3 3 3 4 5 15 7 1 ...
  ..$ raw_clonotype_id: chr [1:3823] "clonotype81" "clonotype81" "clonotype289" "clonotype289" ...
  ..$ raw_consensus_id: chr [1:3823] "clonotype81_consensus_1" "clonotype81_consensus_2" "clonotype289_consensus_2" "clonotype289_consensus_1" ...
 $ :'data.frame':   3855 obs. of  18 variables:
  ..$ barcode         : chr [1:3855] "AAACCTGAGAGACTAT-1" "AAACCTGAGGACAGAA-1" "AAACCTGAGGACAGAA-1" "AAACCTGAGGTGTTAA-1" ...
  ..$ is_cell         : chr [1:3855] "true" "true" "true" "true" ...
  ..$ contig_id       : chr [1:3855] "AAACCTGAGAGACTAT-1_contig_1" "AAACCTGAGGACAGAA-1_contig_1" "AAACCTGAGGACAGAA-1_contig_2" "AAACCTGAGGTGTTAA-1_contig_1" ...
  ..$ high_confidence : chr [1:3855] "true" "true" "true" "true" ...
  ..$ length          : int [1:3855] 559 547 499 501 476 685 518 540 470 526 ...
  ..$ chain           : chr [1:3855] "TRA" "TRA" "TRB" "TRB" ...
  ..$ v_gene          : chr [1:3855] "TRAV21" "TRAV21" "TRBV7-9" "TRBV27" ...
  ..$ d_gene          : chr [1:3855] "" "" "" "TRBD2" ...
  ..$ j_gene          : chr [1:3855] "TRAJ45" "TRAJ43" "TRBJ1-4" "TRBJ2-7" ...
  ..$ c_gene          : chr [1:3855] "TRAC" "TRAC" "TRBC1" "TRBC2" ...
  ..$ full_length     : chr [1:3855] "true" "true" "true" "true" ...
  ..$ productive      : chr [1:3855] "true" "true" "true" "true" ...
  ..$ cdr3            : chr [1:3855] "CAVSLYSGGGADGLTF" "CAVKGYMSNDMRF" "CASSLRPGTGPNEKLFF" "CASRGTGTSGSLAEQYF" ...
  ..$ cdr3_nt         : chr [1:3855] "TGTGCTGTGAGTTTGTATTCAGGAGGAGGTGCTGACGGACTCACCTTT" "TGTGCTGTGAAGGGTTATATGAGCAATGACATGCGCTTT" "TGTGCCAGCAGCCTTCGTCCCGGGACAGGACCGAATGAAAAACTGTTTTTT" "TGTGCCAGCAGGGGGACCGGCACTAGCGGGAGTTTAGCCGAGCAGTACTTC" ...
  ..$ reads           : int [1:3855] 940 394 1574 1430 3553 1218 1726 478 1872 3653 ...
  ..$ umis            : int [1:3855] 2 1 2 4 5 4 5 1 2 5 ...
  ..$ raw_clonotype_id: chr [1:3855] "clonotype17" "clonotype5" "clonotype5" "clonotype63" ...
  ..$ raw_consensus_id: chr [1:3855] "clonotype17_consensus_1" "clonotype5_consensus_2" "clonotype5_consensus_1" "clonotype63_consensus_1" ...
 $ :'data.frame':   4483 obs. of  18 variables:
  ..$ barcode         : chr [1:4483] "AAACCTGAGTGTCTCA-1" "AAACCTGAGTGTCTCA-1" "AAACCTGCAGCTCCGA-1" "AAACCTGCAGCTCCGA-1" ...
  ..$ is_cell         : chr [1:4483] "true" "true" "true" "true" ...
  ..$ contig_id       : chr [1:4483] "AAACCTGAGTGTCTCA-1_contig_1" "AAACCTGAGTGTCTCA-1_contig_2" "AAACCTGCAGCTCCGA-1_contig_1" "AAACCTGCAGCTCCGA-1_contig_2" ...
  ..$ high_confidence : chr [1:4483] "true" "true" "true" "true" ...
  ..$ length          : int [1:4483] 529 466 508 522 552 501 459 494 492 536 ...
  ..$ chain           : chr [1:4483] "TRA" "TRB" "TRB" "TRA" ...
  ..$ v_gene          : chr [1:4483] "TRAV14/DV4" "TRBV28" "TRBV12-4" "TRAV21" ...
  ..$ d_gene          : chr [1:4483] "" "" "" "" ...
  ..$ j_gene          : chr [1:4483] "TRAJ3" "TRBJ1-1" "TRBJ2-1" "TRAJ13" ...
  ..$ c_gene          : chr [1:4483] "TRAC" "TRBC1" "TRBC2" "TRAC" ...
  ..$ full_length     : chr [1:4483] "true" "true" "true" "true" ...
  ..$ productive      : chr [1:4483] "true" "true" "true" "true" ...
  ..$ cdr3            : chr [1:4483] "CAMREREYSSASKIIF" "CASRPTGNTEAFF" "CASSLEGSNEQFF" "CAVRPSGGYQKVTF" ...
  ..$ cdr3_nt         : chr [1:4483] "TGTGCAATGAGAGAGAGGGAGTACAGCAGTGCTTCCAAGATAATCTTT" "TGTGCCAGCAGACCTACAGGGAACACTGAAGCTTTCTTT" "TGTGCCAGCAGTTTGGAGGGGAGTAATGAGCAGTTCTTC" "TGTGCTGTGAGGCCATCTGGGGGTTACCAGAAAGTTACCTTT" ...
  ..$ reads           : int [1:4483] 494 3153 1211 1788 2537 982 767 731 2237 3865 ...
  ..$ umis            : int [1:4483] 1 10 6 3 9 3 2 1 4 13 ...
  ..$ raw_clonotype_id: chr [1:4483] "clonotype6" "clonotype6" "clonotype570" "clonotype570" ...
  ..$ raw_consensus_id: chr [1:4483] "clonotype6_consensus_2" "clonotype6_consensus_1" "clonotype570_consensus_1" "clonotype570_consensus_2" ...

.I was wondering what could be wrong and how to solve the problem.

Thank you

[sudeshna]

The problem has been solved. In my dataset, the columns is_cell =" true" and productive ="true" are in lowercase. For the function combineTCR to work, it should be in uppercase - is_cell =" TRUE" and productive ="TRUE"