Given a repertoire_id table, for each generate rarefaction curves to estimate repertoire diversity. The method used to generate the rarefaction curve is derived from Chao et al., (2014) using the iNEXT library
Arguments
- sample_table
A tibble consisting antigen receptor sequencing data imported by the LymphoSeq2 function readImmunoSeq. "junction_aa", "duplicate_count", and "duplicate_frequency" are required columns.
Examples
library(magrittr)
file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1) %>%
LymphoSeq2::topSeqs(top = 100)
amino_table <- LymphoSeq2::productiveSeq(study_table,
aggregate = "junction_aa",
prevalence = TRUE
)
amino_table <- amino_table %>%
dplyr::filter(repertoire_id == "TRB_Unsorted_1320")
rarefaction_table <- LymphoSeq2::runINext(amino_table)