tests/testthat/test_prodseq.R

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

context("Get productive sequences")
library(LymphoSeq2)

test_that("Gather productive aminoacid sequences", {
  stable <- LymphoSeq2::readImmunoSeq(c("test_data/015V12001549_CFAR.tsv", 
                                        "test_data/015V12001685_CFAR_R.tsv"))
  atable <- LymphoSeq2::productiveSeq(stable)
  arow <- base::nrow(atable)
  ctable <- tibble::tibble(repertoire_id = c("015V12001549_CFAR", "015V12001685_CFAR_R"),
                           tot_freq = c(1, 1),
                           nrows = c(40, 38),
                           nnuc = c(40, 38)) %>%
            dplyr::mutate(nrows = base::as.integer(nrows),
                          nnuc = base::as.integer(nnuc))
  atable <- atable %>% 
            dplyr::group_by(repertoire_id) %>% 
            dplyr::summarize(tot_freq = base::sum(duplicate_frequency), 
                             nrows = dplyr::n(), 
                             nnuc = base::length(base::unique(junction_aa)))
  expect_equal(arow, 78)
  expect_true(dplyr::all_equal(ctable, atable))
})

test_that("Gather productive nucleotide sequences", {
  stable <- LymphoSeq2::readImmunoSeq(c("test_data/015V12001549_CFAR.tsv", 
                                        "test_data/015V12001685_CFAR_R.tsv"))
  atable <- LymphoSeq2::productiveSeq(stable, aggregate = "junction")
  arow <- base::nrow(atable)
  ctable <- tibble::tibble(repertoire_id = c("015V12001549_CFAR", "015V12001685_CFAR_R"),
                           tot_freq = c(1, 1),
                           nrows = c(40, 38),
                           nnuc = c(40, 38)) %>%
            dplyr::mutate(nrows = base::as.integer(nrows),
                          nnuc = base::as.integer(nnuc))
  atable <- atable %>% 
            dplyr::group_by(repertoire_id) %>% 
            dplyr::summarize(tot_freq = base::sum(duplicate_frequency), 
                             nrows = dplyr::n(), 
                             nnuc = base::length(base::unique(junction_aa)))
  expect_equal(arow, 78)
  expect_true(dplyr::all_equal(ctable, atable))
})


test_that("Count of collapse amino acid sequences match", {
  stable <- LymphoSeq2::readImmunoSeq("test_data/015V06013979_CFAR.tsv")
  atable <- LymphoSeq2::productiveSeq(stable, aggregate = "junction_aa")
  ctable <- tibble::tibble(repertoire_id = c("015V06013979_CFAR", "015V06013979_CFAR"),
                           junction_aa = c("CAIEGRGHSDTQYF", "CAIPEREGTDDYGYTF"),
                           duplicate_count = c(3, 361))
  atable <- atable %>% 
            dplyr::filter(junction_aa %in% c("CAIEGRGHSDTQYF", "CAIPEREGTDDYGYTF")) %>%
            dplyr::select(repertoire_id, junction_aa, duplicate_count)
  expect_true(dplyr::all_equal(ctable, atable))
})


test_that("Prevalence of amino acid sequences is correct", {
  stable <- LymphoSeq2::readImmunoSeq("test_data")
  ntable <- LymphoSeq2::productiveSeq(stable, aggregate = "junction_aa", prevalence = TRUE) %>% 
            dplyr::select(prevalence, junction_aa) %>%
            dplyr::filter(prevalence != 0) %>%
            dplyr::arrange(junction_aa) %>%
            dplyr::distinct() 
  junction_list <- ntable %>% dplyr::pull(junction_aa) %>% base::unique()
  prevalenceTRB <- LymphoSeq2::prevalenceTRB %>%
                   dplyr::rename(junction_aa = "aminoAcid") %>%
                   dplyr::filter(junction_aa %in% junction_list)
  expect_true(dplyr::all_equal(prevalenceTRB, ntable))
})