tests/testthat/test.toydata.R

In CB2: CRISPR Pooled Screen Analysis using Beta-Binomial Test

context("Check whether it works")

library(CB2)
library(dplyr)
library(tidyr)
library(tibble)
library(dplyr)
library(magrittr)
FASTA <- system.file("extdata",
                     "toydata", "small_sample_dup.fasta",
                     package = "CB2")
df_design <- data.frame()
for(g in c("Low", "High", "Base")) {
  for(i in 1:2) {
    FASTQ <- system.file("extdata", "toydata",
                         sprintf("%s%d.fastq", g, i), 
                         package = "CB2")
    df_design <- rbind(df_design, 
                       data.frame(
                         group = g, 
                         sample_name = sprintf("%s%d", g, i),
                         fastq_path = FASTQ, 
                         stringsAsFactors = F)
    )
  }
}

rep.row <- function(x,n) matrix(rep(x,each=n),nrow=n)


test_that("A very simple sanity check", {
  expect_length((cb2_count <- run_sgrna_quant(FASTA, df_design)), 3)
  expect_error(run_sgrna_quant(FASTA, df_design[,c("group", "sample_name")]))
  expect_length((sgstat <- measure_sgrna_stats(cb2_count$count, df_design, "Base", "Low")), 19)
  expect_error(measure_sgrna_stats(cb2_count$count, df_design, "Base", "Lows"),  "group_b must be one of the groups in the design data frame.")
  expect_error(measure_sgrna_stats(cb2_count$count, df_design, "Bae", "Low"),  "group_a must be one of the groups in the design data frame.")  
  expect_error(measure_sgrna_stats(cb2_count$count[,-1], df_design, "Bae", "Low"),  "Some samples are missing in sgcount.")  
  expect_length(measure_gene_stats(sgstat), 11)
  expect_error(measure_gene_stats(cb2_count$count), "It looks like `sgrna_stat` does not contain any result of a statistical test.")
  
  expect_error(measure_sgrna_stats(cb2_count, df_design, "Base", "Low"),  "sgcount has to be either a data.frame or a matrix.")
  
})

test_that("Check whether CB2 can handle gzipped file", {
  df_design_gz <- data.frame()
  for(g in c("Low", "High", "Base")) {
    for(i in 1:2) {
      FASTQ <- system.file("extdata", "toydata", "gzipped",
                           sprintf("%s%d.fastq.gz", g, i), 
                           package = "CB2")
      df_design_gz <- rbind(df_design_gz, 
                         data.frame(
                           group = g, 
                           sample_name = sprintf("%s%d", g, i),
                           fastq_path = FASTQ, 
                           stringsAsFactors = F)
      )
    }
  }
  
  expect_length((cb2_count <- run_sgrna_quant(FASTA, df_design)), 3)
  expect_length((cb2_count_gz <- run_sgrna_quant(FASTA, df_design_gz)), 3)
  
  testthat::expect_true(all(cb2_count_gz$count == cb2_count$count))
})


test_that("Test parallelized quantification.", {
    testthat::expect_length(run_sgrna_quant(FASTA, df_design, ncores = 1), 3)
    #testthat::expect_length(run_sgrna_quant(FASTA, df_design, ncores = -1), 3)
    testthat::expect_length(run_sgrna_quant(FASTA, df_design, ncores = 2), 3)
})

#test_that("The result has to be consistent to the publication", {
#  data("Sanson_CRISPRn_A375")
#  published <- read.csv("https://raw.githubusercontent.com/hyunhwaj/CB2-Experiments/master/01_gene-level-analysis/results/Sanson/CRISPRn-A375/FDR/CB2.csv")
#  sgrna <- measure_sgrna_stats(Sanson_CRISPRn_A375$count, Sanson_CRISPRn_A375$design, "ctl", "trt")
#  gene <- measure_gene_stats(sgrna)
#
#  test <- dplyr::left_join(
#    published,
#    gene %>% select(gene, fdr_test = fdr_pa)
#  )
#
#  testthat::expect_true(sum(abs(test$fdr-test$fdr_test)) < 1e-10, "failed to reproduce the publication result.")
#})

test_that("It should allow a table with two columns contains sgRNA information", {
  data(Evers_CRISPRn_RT112)
  df_cb2 <- separate(rownames_to_column(Evers_CRISPRn_RT112$count, "gRNA"), "gRNA", c("gene", "id"))
  testthat::expect_type(
    measure_sgrna_stats(df_cb2, Evers_CRISPRn_RT112$design, "before", "after", ge_id = "gene", sg_id = "id"),
    "list"
  )
})


test_that("Testing error handling of the measure_sgrna_stats.", {
  data(Evers_CRISPRn_RT112)
  df_cb2 <- separate(rownames_to_column(Evers_CRISPRn_RT112$count, "gRNA"), "gRNA", c("gene", "id"))
  
  
  expect_error(measure_sgrna_stats(df_cb2, Evers_CRISPRn_RT112$design, "before", "after"),  
               paste0("sgcount contains some character columns. ", 
                      "It may need to specify both ge_id and sg_id."))
  
  expect_error(measure_sgrna_stats(Evers_CRISPRn_RT112$count, 
                                   Evers_CRISPRn_RT112$design, 
                                   "before", "after", "-"),  
               "Every rownames should contains exact one delimiter.")
  
  expect_error(measure_sgrna_stats(Evers_CRISPRn_RT112$count, 
                                   Evers_CRISPRn_RT112$design, 
                                   "before", "after", 
                                   ge_id = "A"),  
               "Both of ge_id and sg_id should be null or non-null.")
  
  expect_error(measure_sgrna_stats(df_cb2, Evers_CRISPRn_RT112$design, 
                                   "before", "after", ge_id = c("A", "B"),
                                   sg_id = c("A", "B")),  
               "ge_id should be a character variables")
})


test_that("Testing logFC calculation of the measure_sgrna_stats.", {
  data(Evers_CRISPRn_RT112)
  sg <- measure_sgrna_stats(Evers_CRISPRn_RT112$count, Evers_CRISPRn_RT112$design, "before", "after")
  
  expect_error(measure_gene_stats(sg, logFC_level = "sg"),
               "logFC_level` has to be 'gene' or 'sgRNA'.")
  
  ge <- measure_gene_stats(sg, logFC_level = "sgRNA")
  
  sg_logFC <- ge %>% group_by(gene) %>% 
    summarise(logFC = mean(logFC)) %>% 
    ungroup() %>% pull(logFC)
  expect_equal(ge$logFC, sg_logFC, tolerance = 1e-8)
  
  ge_logFC <- ge %>% group_by(gene) %>% 
    summarise(cpm_a = mean(cpm_a), cpm_b = mean(cpm_b)) %>% 
    ungroup() %>% 
    mutate(logFC = log2(cpm_b+1) - log2(cpm_a+1)) %>% 
    pull(logFC)

  ge <- measure_gene_stats(sg, logFC_level = "gene")
  
  expect_equal(ge$logFC, ge_logFC, tolerance = 1e-8)
})