Creates a data frame of VDJ gene counts and frequencies.
Arguments
- nucleotide_table
A tibble of productive sequences generated by the LymphoSeq2 function
productiveSeq()where the parameter aggregate is set to "junction".- locus
A character vector indicating which VDJ genes to include in the output. Available options include
"VDJ","DJ","VJ","DJ","V","D", or"J".- family
A Boolean value indicating whether or not family names instead of gene names are used. If TRUE, then family names are used and if FALSE, gene names are used.
Examples
file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
nucleotide_table <- LymphoSeq2::productiveSeq(study_table = study_table,
aggregate = "junction")
LymphoSeq2::geneFreq(nucleotide_table, locus = "VDJ", family = FALSE)
#> # A tibble: 416 × 5
#> repertoire_id gene_name duplicate_count gene_type gene_frequency
#> <chr> <chr> <dbl> <chr> <dbl>
#> 1 TRB_CD4_949 NA 4419 d_call 0.255
#> 2 TRB_CD4_949 TRBD1-1 5584 d_call 0.322
#> 3 TRB_CD4_949 TRBD2-1 7323 d_call 0.423
#> 4 TRB_CD4_949 TRBJ1-1 525 j_call 0.0365
#> 5 TRB_CD4_949 TRBJ1-2 944 j_call 0.0656
#> 6 TRB_CD4_949 TRBJ1-3 2083 j_call 0.145
#> 7 TRB_CD4_949 TRBJ1-4 267 j_call 0.0186
#> 8 TRB_CD4_949 TRBJ1-5 1057 j_call 0.0735
#> 9 TRB_CD4_949 TRBJ1-6 1552 j_call 0.108
#> 10 TRB_CD4_949 TRBJ2-1 614 j_call 0.0427
#> # ℹ 406 more rows