runINext: Run iNEXT on repertoire_ids

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Run iNEXT on repertoire_ids

Description

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

Usage

runINext(sample_table)

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

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)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.