Mutate scRepertorie object
Alias of MutateScRep
Arguments
- screp
The scRepertorie object. It is either a Seurat object or a list of data.frames
- mutaters
A named list of mutater expressions, where the names are the new column names and the values are the expressions to mutate the columns The name with the suffix
:identwill be used as the new identity column (only for Seurat object) The values can be either character strings of expressions to be parsed- log
Logger object to log the messages. If NULL, the default logger will be used.
Examples
# \donttest{
data(contig_list, package = "scRepertoire")
screp <- scRepertoire::combineTCR(contig_list)
head(MutateScRep(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
# }