Returns all of the paired TCRs from all samples in a dataset
get_all_tcrs.Rd![[Experimental]](figures/lifecycle-experimental.svg)
The get_all_tcrs() function aggregates the TCRs from all samples of a dataset
and puts them into one table.
Usage
get_all_tcrs(
data,
chain = c("paired", "alpha", "beta"),
remove_duplicates = TRUE
)Arguments
- data
a TIRTLseqDataSet object created by
load_tirtlseq()- chain
the TCR chain, "alpha", "beta", or "paired" (default is paired)
- remove_duplicates
only return one TCR for TCRs paired by both the T-SHELL and MAD-HYPE algorithms (default is TRUE).
Details
A pair of TCRs is included twice in the TIRTLseq data if it is recognized by both the T-SHELL and MAD-HYPE algorithms. If remove_duplicates is TRUE (default) the function will only return one of these pairs of TCRs.
See also
Examples
folder = system.file("extdata/SJTRC_TIRTL_seq_longitudinal", package = "TIRTLtools")
ts_data = load_tirtlseq(folder, meta_columns = c("marker", "timepoint", "version"), sep = "_", verbose = FALSE)
get_all_tcrs(ts_data, chain = "paired")
#> Key: <beta_nuc>
#> method va ja cdr3a cdr3b vb
#> <char> <char> <char> <char> <char> <char>
#> 1: tshell TRAV21 TRAJ39 CAVNAGNMLTF CSGTANTGELFF TRBV29-1
#> 2: madhype TRAV23/DV6 TRAJ40 CAAQSGTYKYIF CSALAKNIQYF TRBV29-1
#> 3: madhype TRAV9-2 TRAJ10 CALSDWGTGGGNKLTF CSAGTSVETQYF TRBV29-1
#> 4: madhype TRAV8-6 TRAJ23 CAVTHIT_GGKLIF CSAGTSVETQYF TRBV29-1
#> 5: madhype TRAV34 TRAJ54 CGPLQGAQKLVF CASRVDGYNEQFF TRBV5-1
#> ---
#> 165667: madhype TRAV19 TRAJ58 CALSEASGSRLTF CSAQLAA_FGDTQYF TRBV20-1
#> 165668: madhype TRAV8-6 TRAJ48 CAVTPLDFRNEKLTF CASSIFPG_RDPRGAVF TRBV5-1
#> 165669: madhype TRAV13-2 TRAJ26 CAENHGQNFVF CASSATSR_PTLEQYF TRBV7-3
#> 165670: madhype TRAV6 TRAJ37 CALDTSNTGKLIF CASSPDR_HRELFF TRBV6-4
#> 165671: tshell TRAV14/DV4 TRAJ24 CAMRESAYWGKLQF CASSLPI*REASGANVLTF TRBV27
#> jb alpha_rank beta_rank alpha_readFraction beta_readFraction
#> <char> <int> <int> <num> <num>
#> 1: TRBJ2-2 8 1 3.812515e-04 1.379590e-03
#> 2: TRBJ2-4 214 2 1.026169e-04 8.040853e-04
#> 3: TRBJ2-5 94 3 1.406358e-04 5.757980e-04
#> 4: TRBJ2-5 2294 3 2.747121e-05 5.757980e-04
#> 5: TRBJ2-1 34 4 2.205174e-04 5.147174e-04
#> ---
#> 165667: TRBJ2-3 8434 492846 7.748581e-06 3.614594e-08
#> 165668: TRBJ2-2 322671 493012 2.034638e-07 3.614594e-08
#> 165669: TRBJ2-7 182443 493305 9.494979e-07 3.614594e-08
#> 165670: TRBJ2-2 206907 497592 7.629894e-07 3.614594e-08
#> 165671: TRBJ2-6 176039 497698 1.000364e-06 3.614594e-08
#> alpha_readCount beta_readCount is_functional
#> <int> <int> <lgcl>
#> 1: 29061 145569 TRUE
#> 2: 7822 84844 TRUE
#> 3: 10720 60756 TRUE
#> 4: 2094 60756 FALSE
#> 5: 16809 54311 TRUE
#> ---
#> 165667: 457 3 FALSE
#> 165668: 12 3 FALSE
#> 165669: 56 3 FALSE
#> 165670: 45 3 FALSE
#> 165671: 59 3 FALSE
#> alpha_nuc
#> <char>
#> 1: TGTGCTGTGAACGCAGGCAACATGCTCACCTTT
#> 2: TGTGCAGCTCAATCAGGAACCTACAAATACATCTTT
#> 3: TGTGCTCTGAGTGATTGGGGGACGGGAGGAGGAAACAAACTCACCTTT
#> 4: TGTGCTGTGACCCATATAACCAGGGAGGAAAGCTTATCTTC
#> 5: TGTGGACCTCTTCAGGGAGCCCAGAAGCTGGTATTT
#> ---
#> 165667: TGTGCTCTGAGTGAGGCCAGTGGCTCTAGGTTGACCTTT
#> 165668: TGTGCTGTGACTCCCCTCGACTTTAGAAATGAGAAATTAACCTTT
#> 165669: TGTGCAGAGAACCATGGTCAGAATTTTGTCTTT
#> 165670: TGTGCTCTAGACACAAGCAACACAGGCAAACTAATCTTT
#> 165671: TGTGCAATGAGAGAGTCCGCTTACTGGGGGAAATTGCAGTTT
#> beta_nuc
#> <char>
#> 1: TGCAGCGGGACAGCGAACACCGGGGAGCTGTTTTTT
#> 2: TGCAGCGCATTAGCCAAAAACATTCAGTACTTC
#> 3: TGCAGCGCCGGGACTAGCGTGGAGACCCAGTACTTC
#> 4: TGCAGCGCCGGGACTAGCGTGGAGACCCAGTACTTC
#> 5: TGCGCCAGCAGAGTCGATGGCTACAATGAGCAGTTCTTC
#> ---
#> 165667: TGCAGTGCTCAGCTAGCGGCTTTTTCGGGGATACGCAGTATTTT
#> 165668: TGCGCCAGCAGCATCTTTCCGGGACAGAGATCCCCGGGGAGCTGTTTTT
#> 165669: TGCGCCAGCAGCGCTACGTCCAGACACCTACTTTAGAGCAGTACTTC
#> 165670: TGTGCCAGCAGTCCCGACAGGGACACCGGGAGCTGTTTTTT
#> 165671: TGTGCCAGCAGTCTACCAATCTAGCGGGAGGCATCTGGGGCCAACGTCCTGACTTTC
#> alpha_beta
#> <char>
#> 1: TGTGCTGTGAACGCAGGCAACATGCTCACCTTT_TGCAGCGGGACAGCGAACACCGGGGAGCTGTTTTTT
#> 2: TGTGCAGCTCAATCAGGAACCTACAAATACATCTTT_TGCAGCGCATTAGCCAAAAACATTCAGTACTTC
#> 3: TGTGCTCTGAGTGATTGGGGGACGGGAGGAGGAAACAAACTCACCTTT_TGCAGCGCCGGGACTAGCGTGGAGACCCAGTACTTC
#> 4: TGTGCTGTGACCCATATAACCAGGGAGGAAAGCTTATCTTC_TGCAGCGCCGGGACTAGCGTGGAGACCCAGTACTTC
#> 5: TGTGGACCTCTTCAGGGAGCCCAGAAGCTGGTATTT_TGCGCCAGCAGAGTCGATGGCTACAATGAGCAGTTCTTC
#> ---
#> 165667: TGTGCTCTGAGTGAGGCCAGTGGCTCTAGGTTGACCTTT_TGCAGTGCTCAGCTAGCGGCTTTTTCGGGGATACGCAGTATTTT
#> 165668: TGTGCTGTGACTCCCCTCGACTTTAGAAATGAGAAATTAACCTTT_TGCGCCAGCAGCATCTTTCCGGGACAGAGATCCCCGGGGAGCTGTTTTT
#> 165669: TGTGCAGAGAACCATGGTCAGAATTTTGTCTTT_TGCGCCAGCAGCGCTACGTCCAGACACCTACTTTAGAGCAGTACTTC
#> 165670: TGTGCTCTAGACACAAGCAACACAGGCAAACTAATCTTT_TGTGCCAGCAGTCCCGACAGGGACACCGGGAGCTGTTTTTT
#> 165671: TGTGCAATGAGAGAGTCCGCTTACTGGGGGAAATTGCAGTTT_TGTGCCAGCAGTCTACCAATCTAGCGGGAGGCATCTGGGGCCAACGTCCTGACTTTC
#> wi wj wij wa wb score r ts
#> <int> <int> <int> <int> <int> <num> <num> <num>
#> 1: 0 24 166 166 190 -5.46801297 0.9433375 39.08193
#> 2: 1 58 110 111 168 2.22849497 NA NA
#> 3: 1 65 76 77 141 6.17941220 NA NA
#> 4: 3 73 68 71 141 2.22543597 NA NA
#> 5: 4 16 151 155 167 7.40350947 NA NA
#> ---
#> 165667: 0 0 3 3 3 0.60578435 NA NA
#> 165668: 0 0 3 3 3 0.60578435 NA NA
#> 165669: 0 0 3 3 3 0.60578435 NA NA
#> 165670: 0 0 3 3 3 0.60578435 NA NA
#> 165671: 1 0 3 4 3 0.06720111 0.9371988 37.03713
#> pval pval_adj loss_a_frac loss_b_frac alpha_readCount_max
#> <num> <num> <num> <num> <int>
#> 1: 1.747597e-92 6.346881e-84 0.12631579 0.000000000 467
#> 2: NA NA 0.34319527 0.005917160 318
#> 3: NA NA 0.45774648 0.007042254 399
#> 4: NA NA 0.50694444 0.020833333 172
#> 5: NA NA 0.09356725 0.023391813 380
#> ---
#> 165667: NA NA 0.00000000 0.000000000 214
#> 165668: NA NA 0.00000000 0.000000000 6
#> 165669: NA NA 0.00000000 0.000000000 39
#> 165670: NA NA 0.00000000 0.000000000 29
#> 165671: 7.557454e-89 1.735806e-53 0.00000000 0.250000000 21
#> alpha_readCount_median alpha_sem alpha_max_wells beta_readCount_max
#> <num> <num> <int> <int>
#> 1: 167.5 2.012317e-05 191 2501
#> 2: 55.0 1.011121e-05 191 2483
#> 3: 117.0 1.598201e-05 191 2334
#> 4: 24.0 3.776374e-06 191 2334
#> 5: 78.0 1.505977e-05 191 1270
#> ---
#> 165667: 135.0 3.696180e-06 192 1
#> 165668: 5.0 1.059311e-07 192 1
#> 165669: 10.0 9.904153e-07 192 1
#> 165670: 11.0 5.662021e-07 192 1
#> 165671: 13.0 5.283245e-07 192 1
#> beta_readCount_median beta_sem beta_max_wells alpha_has_stop_codon
#> <num> <num> <int> <lgcl>
#> 1: 739.5 7.132553e-05 191 FALSE
#> 2: 391.5 6.976097e-05 191 FALSE
#> 3: 150.0 6.087061e-05 191 FALSE
#> 4: 150.0 6.087061e-05 191 FALSE
#> 5: 278.0 3.137988e-05 191 FALSE
#> ---
#> 165667: 1.0 1.727190e-08 192 FALSE
#> 165668: 1.0 1.698039e-08 192 FALSE
#> 165669: 1.0 2.308962e-08 192 FALSE
#> 165670: 1.0 2.047129e-08 192 FALSE
#> 165671: 1.0 2.384106e-08 192 FALSE
#> alpha_has_frameshift beta_has_stop_codon beta_has_frameshift
#> <lgcl> <lgcl> <lgcl>
#> 1: FALSE FALSE FALSE
#> 2: FALSE FALSE FALSE
#> 3: FALSE FALSE FALSE
#> 4: TRUE FALSE FALSE
#> 5: FALSE FALSE FALSE
#> ---
#> 165667: FALSE FALSE TRUE
#> 165668: FALSE FALSE TRUE
#> 165669: FALSE FALSE TRUE
#> 165670: FALSE FALSE TRUE
#> 165671: FALSE TRUE FALSE
#> alpha_is_functional beta_is_functional alpha_id beta_id
#> <lgcl> <lgcl> <char> <char>
#> 1: TRUE TRUE alpha_8 beta_1
#> 2: TRUE TRUE alpha_214 beta_2
#> 3: TRUE TRUE alpha_94 beta_3
#> 4: FALSE TRUE alpha_2294 beta_3
#> 5: TRUE TRUE alpha_34 beta_4
#> ---
#> 165667: TRUE FALSE alpha_8434 beta_492846
#> 165668: TRUE FALSE alpha_322671 beta_493012
#> 165669: TRUE FALSE alpha_182443 beta_493305
#> 165670: TRUE FALSE alpha_206907 beta_497592
#> 165671: TRUE FALSE alpha_176039 beta_497698
#> receptor_rank receptor_id sample_id marker timepoint version
#> <int> <char> <char> <char> <char> <char>
#> 1: 1 receptor_1 cd4_tp1_v2 cd4 tp1 v2
#> 2: 2 receptor_2 cd4_tp1_v2 cd4 tp1 v2
#> 3: 3 receptor_3 cd4_tp1_v2 cd4 tp1 v2
#> 4: 3 receptor_3 cd4_tp1_v2 cd4 tp1 v2
#> 5: 4 receptor_4 cd4_tp1_v2 cd4 tp1 v2
#> ---
#> 165667: 492846 receptor_492846 cd8_tp3_v2 cd8 tp3 v2
#> 165668: 493012 receptor_493012 cd8_tp3_v2 cd8 tp3 v2
#> 165669: 493305 receptor_493305 cd8_tp3_v2 cd8 tp3 v2
#> 165670: 497592 receptor_497592 cd8_tp3_v2 cd8 tp3 v2
#> 165671: 497698 receptor_497698 cd8_tp3_v2 cd8 tp3 v2
#> label
#> <char>
#> 1: marker: cd4 | timepoint: tp1 | version: v2
#> 2: marker: cd4 | timepoint: tp1 | version: v2
#> 3: marker: cd4 | timepoint: tp1 | version: v2
#> 4: marker: cd4 | timepoint: tp1 | version: v2
#> 5: marker: cd4 | timepoint: tp1 | version: v2
#> ---
#> 165667: marker: cd8 | timepoint: tp3 | version: v2
#> 165668: marker: cd8 | timepoint: tp3 | version: v2
#> 165669: marker: cd8 | timepoint: tp3 | version: v2
#> 165670: marker: cd8 | timepoint: tp3 | version: v2
#> 165671: marker: cd8 | timepoint: tp3 | version: v2