Mutate scRepertorie object

Usage

ScRepMutate(screp, mutaters)

Arguments

screp: The scRepertorie object. It is either a Seurat object or a list of data.frames
mutaters: A list of expressions (in characters) to mutate the data

Value

The mutated scRepertorie object

Examples

# \donttest{
data(contig_list, package = "scRepertoire")
screp <- scRepertoire::combineTCR(contig_list)
head(ScRepMutate(screp, list(CTaa_len = "nchar(CTaa)"))[[1]])
#>               barcode                     TCR1           cdr3_aa1
#> 1  AAACCTGAGTACGACG-1       TRAV25.TRAJ20.TRAC        CGCSNDYKLSF
#> 3  AAACCTGCAACACGCC-1 TRAV38-2/DV8.TRAJ52.TRAC CAYRSAQAGGTSYGKLTF
#> 5  AAACCTGCAGGCGATA-1      TRAV12-1.TRAJ9.TRAC     CVVSDNTGGFKTIF
#> 7  AAACCTGCATGAGCGA-1      TRAV12-1.TRAJ9.TRAC     CVVSDNTGGFKTIF
#> 9  AAACGGGAGAGCCCAA-1        TRAV20.TRAJ8.TRAC      CAVRGEGFQKLVF
#> 10 AAACGGGAGCGTTTAC-1      TRAV12-1.TRAJ9.TRAC     CVVSDNTGGFKTIF
#>                                                  cdr3_nt1
#> 1                       TGTGGGTGTTCTAACGACTACAAGCTCAGCTTT
#> 3  TGTGCTTATAGGAGCGCGCAGGCTGGTGGTACTAGCTATGGAAAGCTGACATTT
#> 5              TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT
#> 7              TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT
#> 9                 TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT
#> 10             TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT
#>                           TCR2          cdr3_aa2
#> 1   TRBV5-1.None.TRBJ2-7.TRBC2    CASSLTDRTYEQYF
#> 3  TRBV10-3.None.TRBJ2-2.TRBC2     CAISEQGKGELFF
#> 5     TRBV9.None.TRBJ2-2.TRBC2 CASSVRRERANTGELFF
#> 7     TRBV9.None.TRBJ2-2.TRBC2 CASSVRRERANTGELFF
#> 9                         <NA>              <NA>
#> 10    TRBV9.None.TRBJ2-2.TRBC2 CASSVRRERANTGELFF
#>                                               cdr3_nt2
#> 1           TGCGCCAGCAGCTTGACCGACAGGACCTACGAGCAGTACTTC
#> 3              TGTGCCATCAGTGAACAGGGGAAAGGGGAGCTGTTTTTT
#> 5  TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#> 7  TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#> 9                                                 <NA>
#> 10 TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#>                                                  CTgene
#> 1         TRAV25.TRAJ20.TRAC_TRBV5-1.None.TRBJ2-7.TRBC2
#> 3  TRAV38-2/DV8.TRAJ52.TRAC_TRBV10-3.None.TRBJ2-2.TRBC2
#> 5          TRAV12-1.TRAJ9.TRAC_TRBV9.None.TRBJ2-2.TRBC2
#> 7          TRAV12-1.TRAJ9.TRAC_TRBV9.None.TRBJ2-2.TRBC2
#> 9                                  TRAV20.TRAJ8.TRAC_NA
#> 10         TRAV12-1.TRAJ9.TRAC_TRBV9.None.TRBJ2-2.TRBC2
#>                                                                                              CTnt
#> 1                    TGTGGGTGTTCTAACGACTACAAGCTCAGCTTT_TGCGCCAGCAGCTTGACCGACAGGACCTACGAGCAGTACTTC
#> 3  TGTGCTTATAGGAGCGCGCAGGCTGGTGGTACTAGCTATGGAAAGCTGACATTT_TGTGCCATCAGTGAACAGGGGAAAGGGGAGCTGTTTTTT
#> 5  TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#> 7  TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#> 9                                                      TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT_NA
#> 10 TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#>                                CTaa
#> 1        CGCSNDYKLSF_CASSLTDRTYEQYF
#> 3  CAYRSAQAGGTSYGKLTF_CAISEQGKGELFF
#> 5  CVVSDNTGGFKTIF_CASSVRRERANTGELFF
#> 7  CVVSDNTGGFKTIF_CASSVRRERANTGELFF
#> 9                  CAVRGEGFQKLVF_NA
#> 10 CVVSDNTGGFKTIF_CASSVRRERANTGELFF
#>                                                                                                                                               CTstrict
#> 1                           TRAV25.TRAJ20.TRAC;TGTGGGTGTTCTAACGACTACAAGCTCAGCTTT_TRBV5-1.None.TRBJ2-7.TRBC2;TGCGCCAGCAGCTTGACCGACAGGACCTACGAGCAGTACTTC
#> 3  TRAV38-2/DV8.TRAJ52.TRAC;TGTGCTTATAGGAGCGCGCAGGCTGGTGGTACTAGCTATGGAAAGCTGACATTT_TRBV10-3.None.TRBJ2-2.TRBC2;TGTGCCATCAGTGAACAGGGGAAAGGGGAGCTGTTTTTT
#> 5          TRAV12-1.TRAJ9.TRAC;TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TRBV9.None.TRBJ2-2.TRBC2;TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#> 7          TRAV12-1.TRAJ9.TRAC;TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TRBV9.None.TRBJ2-2.TRBC2;TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#> 9                                                                                      TRAV20.TRAJ8.TRAC;TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT_NA;NA
#> 10         TRAV12-1.TRAJ9.TRAC;TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TRBV9.None.TRBJ2-2.TRBC2;TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
#>    Sample CTaa_len
#> 1      S1       26
#> 3      S1       32
#> 5      S1       32
#> 7      S1       32
#> 9      S1       16
#> 10     S1       32
# }