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")
#> wi wj wij alpha_nuc
#> <int> <int> <int> <char>
#> 1: 0 0 3 TGTGCCGTGAACGGAGGTAACGACTACAAGCTCAGCTTT
#> 2: 0 0 3 TGTGCTCTTCAAACTTCTGGTGGCTACAATAAGCTGATTTTT
#> 3: 0 0 3 TGTGCTCCCCGGTACACCGGTAACCAGTTCTATTTT
#> 4: 0 0 3 TGTGCAATGAGAGAGGTCGCTTCTGGTGGCTACAATAAGCTGATTTTT
#> 5: 0 0 3 TGTGCTGCCAGCGGGGGCTTTCAGAAACTTGTATTT
#> ---
#> 165667: 94 0 37 TGTGCCGTGGAGGGGGAGTCTGGTGGCTACAATAAGCTGATTTTT
#> 165668: 96 0 50 TGTGCCCCCATGGATAGCAACTATCAGTTAATCTGG
#> 165669: 97 0 36 TGCGCTGTGAGAGATAGGGACACCAATGCAGGCAAATCAACCTTT
#> 165670: 101 0 36 TGTGCAGACGGCCCCCAAGGAAATCTCATCTTT
#> 165671: 103 0 46 TGCGGCACAGAGAGTGGAGGTAGCAACTATAAACTGACATTT
#> beta_nuc wa wb
#> <char> <int> <int>
#> 1: TGTGCCAGCTCACCAGAGCAGGGTCTGGCCCAGCATTTT 3 3
#> 2: TGTGCCAGCAGCTATCAGGGCCAGCAGTTCTTC 3 3
#> 3: TGTGCCATCAGTCGGGGACAGGGGGCAGGTGAGCAGTTCTTC 3 3
#> 4: TGTGCCAGCTCGACAGGGGGACAGCGACCTAATGAAAAACTGTTTTTT 3 3
#> 5: TGCGCCAGCAGCCCAACAGGGGGGCAGGACTATGGCTACACCTTC 3 3
#> ---
#> 165667: TGTGCCAGCAGCGCCCACGGGGAAGGGAACGAAAAACTGTTTTTTT 131 37
#> 165668: TGCAGTGCTAAATTAGCGGGCGACACCGGGGAGCTGTTTTTTT 146 50
#> 165669: TGTGCCAGCAGTTTTTGCGGGGGCGGGCTACGAGCAGTACTTC 133 36
#> 165670: TGTGCCAGCAGTTTTTGCGGGGGCGGGCTACGAGCAGTACTTC 137 36
#> 165671: TGTGCCAGCAGCTGGGACAAAACCTACGAGCAGTACTTC 149 46
#> alpha_beta
#> <char>
#> 1: TGTGCCGTGAACGGAGGTAACGACTACAAGCTCAGCTTT_TGTGCCAGCTCACCAGAGCAGGGTCTGGCCCAGCATTTT
#> 2: TGTGCTCTTCAAACTTCTGGTGGCTACAATAAGCTGATTTTT_TGTGCCAGCAGCTATCAGGGCCAGCAGTTCTTC
#> 3: TGTGCTCCCCGGTACACCGGTAACCAGTTCTATTTT_TGTGCCATCAGTCGGGGACAGGGGGCAGGTGAGCAGTTCTTC
#> 4: TGTGCAATGAGAGAGGTCGCTTCTGGTGGCTACAATAAGCTGATTTTT_TGTGCCAGCTCGACAGGGGGACAGCGACCTAATGAAAAACTGTTTTTT
#> 5: TGTGCTGCCAGCGGGGGCTTTCAGAAACTTGTATTT_TGCGCCAGCAGCCCAACAGGGGGGCAGGACTATGGCTACACCTTC
#> ---
#> 165667: TGTGCCGTGGAGGGGGAGTCTGGTGGCTACAATAAGCTGATTTTT_TGTGCCAGCAGCGCCCACGGGGAAGGGAACGAAAAACTGTTTTTTT
#> 165668: TGTGCCCCCATGGATAGCAACTATCAGTTAATCTGG_TGCAGTGCTAAATTAGCGGGCGACACCGGGGAGCTGTTTTTTT
#> 165669: TGCGCTGTGAGAGATAGGGACACCAATGCAGGCAAATCAACCTTT_TGTGCCAGCAGTTTTTGCGGGGGCGGGCTACGAGCAGTACTTC
#> 165670: TGTGCAGACGGCCCCCAAGGAAATCTCATCTTT_TGTGCCAGCAGTTTTTGCGGGGGCGGGCTACGAGCAGTACTTC
#> 165671: TGCGGCACAGAGAGTGGAGGTAGCAACTATAAACTGACATTT_TGTGCCAGCAGCTGGGACAAAACCTACGAGCAGTACTTC
#> method r ts pval pval_adj loss_a_frac loss_b_frac score
#> <char> <num> <num> <num> <num> <num> <num> <num>
#> 1: madhype NA NA NA NA 0 0.0000000 0.2011610
#> 2: madhype NA NA NA NA 0 0.0000000 0.2011610
#> 3: madhype NA NA NA NA 0 0.0000000 0.2011610
#> 4: madhype NA NA NA NA 0 0.0000000 0.2011610
#> 5: madhype NA NA NA NA 0 0.0000000 0.2011610
#> ---
#> 165667: madhype NA NA NA NA 0 0.7175573 1.5618088
#> 165668: madhype NA NA NA NA 0 0.6575342 1.6288014
#> 165669: madhype NA NA NA NA 0 0.7293233 1.0688280
#> 165670: madhype NA NA NA NA 0 0.7372263 0.5297975
#> 165671: madhype NA NA NA NA 0 0.6912752 0.4727439
#> cdr3a va ja cdr3b vb jb
#> <char> <char> <char> <char> <char> <char>
#> 1: CAVNGGNDYKLSF TRAV12-2 TRAJ20 CASSPEQGLAQHF TRBV18 TRBJ1-5
#> 2: CALQTSGGYNKLIF TRAV9-2 TRAJ4 CASSYQGQQFF TRBV7-6 TRBJ2-1
#> 3: CAPRYTGNQFYF TRAV41 TRAJ49 CAISRGQGAGEQFF TRBV10-3 TRBJ2-1
#> 4: CAMREVASGGYNKLIF TRAV14/DV4 TRAJ4 CASSTGGQRPNEKLFF TRBV6-1 TRBJ1-4
#> 5: CAASGGFQKLVF TRAV2 TRAJ8 CASSPTGGQDYGYTF TRBV5-1 TRBJ1-2
#> ---
#> 165667: CAVEGESGGYNKLIF TRAV12-2 TRAJ4 CASSAHGE_GTKNCFF TRBV9 TRBJ1-4
#> 165668: CAPMDSNYQLIW TRAV1-2 TRAJ33 CSAKLAG_TPGSCFF TRBV20-1 TRBJ2-2
#> 165669: CAVRDRDTNAGKSTF TRAV1-1 TRAJ27 CASSFCG_AGYEQYF TRBV28 TRBJ2-7
#> 165670: CADGPQGNLIF TRAV13-2 TRAJ42 CASSFCG_AGYEQYF TRBV28 TRBJ2-7
#> 165671: CGTESGGSNYKLTF TRAV30 TRAJ53 CASSWDKTYEQYF TRBV5-1 TRBJ2-7
#> sample_id marker timepoint version
#> <char> <char> <char> <char>
#> 1: cd4_tp1_v2 cd4 tp1 v2
#> 2: cd4_tp1_v2 cd4 tp1 v2
#> 3: cd4_tp1_v2 cd4 tp1 v2
#> 4: cd4_tp1_v2 cd4 tp1 v2
#> 5: cd4_tp1_v2 cd4 tp1 v2
#> ---
#> 165667: cd8_tp3_v2 cd8 tp3 v2
#> 165668: cd8_tp3_v2 cd8 tp3 v2
#> 165669: cd8_tp3_v2 cd8 tp3 v2
#> 165670: cd8_tp3_v2 cd8 tp3 v2
#> 165671: 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