Calculate the number and fraction of single chains that were paired by frequency

This function returns the number and fraction of single-chains (alpha or beta, default is beta) that were paired within different frequency ranges (default is [10^-1, 10^-2], [10^-2, 10^-3], ... , [10^-5,10^-6], [10^-6, 0]) for each sample. You can use this function to get the data used in the plot for plot_paired_by_read_fraction_range().

Usage

get_paired_by_read_fraction_range(
  data,
  chain = c("beta", "alpha"),
  cutoffs = 10^(-6:-1)
)

Arguments

data

a TIRTLseqDataSet object

chain

the TCR chain to use for read fraction (default is "beta")

cutoffs

a vector of cutoffs for the read fraction ranges

Value

a data frame with the number and fraction of chains paired for each read fraction range for each sample.

See also

Other qc: get_all_tcrs(), get_pair_stats(), plot_n_reads(), plot_num_partners(), plot_paired(), plot_paired_by_read_fraction_range(), plot_paired_vs_rank(), plot_pairs_with_eachother(), plot_ranks(), plot_read_fraction_vs_pair_status(), plot_sample_overlap(), summarize_data()

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_paired_by_read_fraction_range(ts_data, chain = "beta")
#> # A tibble: 33 × 13
#>    range          n_paired_sum n_paired_sum_tshell n_paired_sum_madhype n_total
#>    <fct>                 <int>               <int>                <int>   <int>
#>  1 [0,1e-06)              6325                2114                 5361 1584466
#>  2 [1e-06,1e-05)         16357               10807                15716  276468
#>  3 [1e-05,0.0001)         6038                4774                 6014    6725
#>  4 [0.0001,0.001)          224                 191                  221     231
#>  5 [0.001,0.01)              1                   1                    0       1
#>  6 [0,1e-06)              4258                1789                 3392 1482037
#>  7 [1e-06,1e-05)         11577                8386                10988  288341
#>  8 [1e-05,0.0001)         4846                3529                 4819    6227
#>  9 [0.0001,0.001)          167                 131                  155     176
#> 10 [0.001,0.01)              1                   1                    0       1
#> # ℹ 23 more rows
#> # ℹ 8 more variables: fraction_paired <dbl>, fraction_paired_tshell <dbl>,
#> #   fraction_paired_madhype <dbl>, sample_id <chr>, marker <chr>,
#> #   timepoint <chr>, version <chr>, label <chr>