tests/testthat/test-diff_deut_uptake_calculations.R

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

dat <- read_hdx(system.file(package = "HaDeX2", "HaDeX/data/KD_180110_CD160_HVEM.csv")) 

################
## REFERENCES ##
################

chosen_protein <- "db_CD160"
chosen_states <- c("CD160", "CD160_HVEM")
chosen_time_0 <- 0.001
chosen_time_100 <- 1440
chosen_time <- 5
deut_part <- 1
chosen_confidence_level <-  0.98

chosen_peptide <- "INITSSASQEGTRLN"
ref_dat <- data.frame(Exposure = c(0.167, 1, 5, 25, 120),
                      diff_deut_uptake = c(0.31887150, 0.34128550, 0.54904750,  0.64388750,   0.10823500),
                      err_diff_deut_uptake = c(0.04604606, 0.09693827, 0.08253328,  0.05494542,   0.08564671),
                      diff_frac_deut_uptake = c(2.49775307, 2.65850667, 4.64333261,  5.51772139,   0.31699929),
                      err_diff_frac_deut_uptake = c(0.77092245, 1.16299771, 1.06350514,  0.91482812,   1.14952706),
                      diff_theo_frac_deut_uptake = c(2.26120002, 2.42014347, 3.89343738,  4.56597227,   0.76752229),
                      err_diff_theo_frac_deut_uptake = c(0.32652445, 0.68741429, 0.58526480,  0.38963213,   0.60734292),
                      diff_theo_deut_uptake = c(0.31887150, 0.34128550, 0.54904750,  0.64388750,   0.10823500),
                      err_diff_theo_deut_uptake = c(0.04604606, 0.09693827, 0.08253328,  0.05494542,   0.08564671))

times <- ref_dat[["Exposure"]]
deut_values <- colnames(ref_dat)[-1]

result_tmp <- data.frame()

###########################
## CALCULATE_DIFF_UPTAKE ##
###########################

lapply(times, function(time){

  result_tmp <- calculate_diff_uptake(dat = dat,
                                      protein = chosen_protein,
                                      states = chosen_states,
                                      time_0 = chosen_time_0,
                                      time_t = time,
                                      time_100 = chosen_time_100,
                                      deut_part = deut_part)
  
  result_tmp <- as.data.table(result_tmp)
  
  lapply(deut_values, function(deut_value){

    test_name <- paste0("calculate_diff_uptake-", time, "min-", deut_value)

    test_that(test_name,
              expect_equal(ref_dat[ref_dat[["Exposure"]] == time, deut_value],
                           result_tmp[result_tmp[["Sequence"]] == chosen_peptide &
                                        result_tmp[["Exposure"]] == time, get(deut_value)]
              )
    )

  })

  # test_that(paste0("data.frame-d calculate_diff_uptake in ", time, "min"), expect_s3_class(result_tmp, "data.frame"))
  
})


################################
## CREATE_DIFF_UPTAKE_DATASET ##
################################

lapply(times, function(time){

  result_tmp <- create_diff_uptake_dataset(dat = dat,
                                           protein = chosen_protein,
                                           state_1 = chosen_states[1],
                                           state_2 = chosen_states[2],
                                           time_0 = chosen_time_0,
                                           time_100 = chosen_time_100,
                                           deut_part = deut_part)
  
  result_tmp <- as.data.table(result_tmp)
  
  lapply(deut_values, function(deut_value){

    test_name <- paste0("create_diff_uptake_dataset-", time, "min-", deut_value)

    test_that(test_name,
              expect_equal(ref_dat[ref_dat[["Exposure"]] == time, deut_value],
                           result_tmp[result_tmp[["Sequence"]] == chosen_peptide &
                                        result_tmp[["Exposure"]] == time, get(deut_value)]
              )
    )

  })

  # test_that(paste0("data.frame-d create_diff_uptake_dataset in ", time, " min"), expect_s3_class(result_tmp, "data.frame"))
  
})


############################
## CREATE_VOLCANO_DATASET ##
############################

## TODO: rewritte
## TODO: test p value

# dat_tmp <- create_volcano_dataset(dat = dat,
#                                   protein = chosen_protein,
#                                   state_1 = chosen_states[1],
#                                   state_2 = chosen_states[2],
#                                   p_adjustment_method = "none",
#                                   confidence_level = chosen_confidence_level)
# 
# lapply(times, function(time){
# 
#   test_name <- paste0("create_volcano_dataset-", time, "min")
# 
#   test_that(test_name,
#             expect_equal(dat_tmp[dat_tmp[["Sequence"]] == chosen_peptide & dat_tmp[["Exposure"]] == time, "D_diff"][[1]],
#                          ref_dat[ref_dat[["Exposure"]] == time, "diff_deut_uptake"]
#             )
#   )
# 
# })