Subset scRepertorie object

Usage

ScRepSubset(screp, subset)

Arguments

screp: The scRepertorie object. It is either a Seurat object or a list of data.frames
subset: The subset expression (in characters)

Value

The subsetted scRepertorie object

Examples

# \donttest{
data(contig_list, package = "scRepertoire")
screp <- scRepertoire::combineTCR(contig_list,
   samples = c("P17B", "P17L", "P18B", "P18L", "P19B","P19L", "P20B", "P20L"))

head(ScRepSubset(screp, "nchar(CTaa) < 20")[[1]])
#>                   barcode sample              TCR1      cdr3_aa1
#> 1 P17B_AAACGGGAGAGCCCAA-1   P17B TRAV20.TRAJ8.TRAC CAVRGEGFQKLVF
#> 2 P17B_AAAGTAGAGGCTACGA-1   P17B              <NA>          <NA>
#> 3 P17B_AAATGCCGTCGACTGC-1   P17B              <NA>          <NA>
#> 4 P17B_AACCATGCAACGATGG-1   P17B              <NA>          <NA>
#> 5 P17B_AACCGCGCACTCGACG-1   P17B              <NA>          <NA>
#> 6 P17B_AACTCAGGTCTAACGT-1   P17B              <NA>          <NA>
#>                                  cdr3_nt1                       TCR2
#> 1 TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT                       <NA>
#> 2                                    <NA> TRBV3-1.None.TRBJ1-1.TRBC1
#> 3                                    <NA> TRBV3-1.None.TRBJ1-1.TRBC1
#> 4                                    <NA>  TRBV27.None.TRBJ2-1.TRBC2
#> 5                                    <NA> TRBV4-3.None.TRBJ1-1.TRBC1
#> 6                                    <NA> TRBV6-2.None.TRBJ2-1.TRBC2
#>           cdr3_aa2                                         cdr3_nt2
#> 1             <NA>                                             <NA>
#> 2   CAAGQGVMNTEAFF       TGTGCCGCGGGGCAGGGGGTCATGAACACTGAAGCTTTCTTT
#> 3   CAAGQGVMNTEAFF       TGTGCCGCGGGGCAGGGGGTCATGAACACTGAAGCTTTCTTT
#> 4 CASSLGSGGTGNEQFF TGTGCCAGCAGTTTAGGGTCGGGGGGGACGGGGAATGAGCAGTTCTTC
#> 5    CASSQDSFTEAFF          TGCGCCAGCAGCCAAGACAGTTTCACTGAAGCTTTCTTT
#> 6 CASSWSKTSGRDEQFF TGTGCCAGCAGTTGGAGTAAGACTAGCGGGAGGGATGAGCAGTTCTTC
#>                          CTgene
#> 1          TRAV20.TRAJ8.TRAC_NA
#> 2 NA_TRBV3-1.None.TRBJ1-1.TRBC1
#> 3 NA_TRBV3-1.None.TRBJ1-1.TRBC1
#> 4  NA_TRBV27.None.TRBJ2-1.TRBC2
#> 5 NA_TRBV4-3.None.TRBJ1-1.TRBC1
#> 6 NA_TRBV6-2.None.TRBJ2-1.TRBC2
#>                                                  CTnt                CTaa
#> 1          TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT_NA    CAVRGEGFQKLVF_NA
#> 2       NA_TGTGCCGCGGGGCAGGGGGTCATGAACACTGAAGCTTTCTTT   NA_CAAGQGVMNTEAFF
#> 3       NA_TGTGCCGCGGGGCAGGGGGTCATGAACACTGAAGCTTTCTTT   NA_CAAGQGVMNTEAFF
#> 4 NA_TGTGCCAGCAGTTTAGGGTCGGGGGGGACGGGGAATGAGCAGTTCTTC NA_CASSLGSGGTGNEQFF
#> 5          NA_TGCGCCAGCAGCCAAGACAGTTTCACTGAAGCTTTCTTT    NA_CASSQDSFTEAFF
#> 6 NA_TGTGCCAGCAGTTGGAGTAAGACTAGCGGGAGGGATGAGCAGTTCTTC NA_CASSWSKTSGRDEQFF
#>                                                                            CTstrict
#> 1                   TRAV20.TRAJ8.TRAC;TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT_NA;NA
#> 2       NA;NA_TRBV3-1.None.TRBJ1-1.TRBC1;TGTGCCGCGGGGCAGGGGGTCATGAACACTGAAGCTTTCTTT
#> 3       NA;NA_TRBV3-1.None.TRBJ1-1.TRBC1;TGTGCCGCGGGGCAGGGGGTCATGAACACTGAAGCTTTCTTT
#> 4  NA;NA_TRBV27.None.TRBJ2-1.TRBC2;TGTGCCAGCAGTTTAGGGTCGGGGGGGACGGGGAATGAGCAGTTCTTC
#> 5          NA;NA_TRBV4-3.None.TRBJ1-1.TRBC1;TGCGCCAGCAGCCAAGACAGTTTCACTGAAGCTTTCTTT
#> 6 NA;NA_TRBV6-2.None.TRBJ2-1.TRBC2;TGTGCCAGCAGTTGGAGTAAGACTAGCGGGAGGGATGAGCAGTTCTTC
#>   Sample
#> 1   P17B
#> 2   P17B
#> 3   P17B
#> 4   P17B
#> 5   P17B
#> 6   P17B
names(ScRepSubset(screp, "Sample %in% c('P17B', 'P17L')"))
#> [1] "P17B" "P17L"
# }