Create a summary table with number of reads and unique alpha/beta chains

This function creates a summary table with the number of reads and unique alpha/beta chains observed for each sample.

Usage

summarize_data(data)

Arguments

data

a TIRTLseqDataSet object

Value

a data frame with the number of reads and unique chains observed for each sample.

See also

Other qc: get_all_tcrs(), get_pair_stats(), get_paired_by_read_fraction_range(), 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()

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)

summarize_data(ts_data)
#> # A tibble: 6 × 6
#>   sample_id  n_alpha_clones n_beta_clones n_clone_pairs n_reads_alpha
#>   <chr>               <int>         <int>         <int>         <int>
#> 1 cd4_tp1_v2        1972376       1867891         47828      76225265
#> 2 cd4_tp2_v2        1966962       1776782         32672      74060977
#> 3 cd4_tp3_v2        2062013       1930208         39012      66235760
#> 4 cd8_tp1_v2         937875        928777         14273      68573045
#> 5 cd8_tp2_v2         980522        895688         17891      68560963
#> 6 cd8_tp3_v2         850578        830552         13995      58978542
#> # ℹ 1 more variable: n_reads_beta <int>