tests/testthat/test-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_state <- "CD160"
chosen_time_0 <- 0.001
chosen_time_100 <- 1440
chosen_time <- 5
deut_part <- 1

chosen_peptide <- "INITSSASQEGTRLN"
chosen_peptide_start <- 1
chosen_peptide_end <- 15

ref_dat <- data.frame(Exposure = c(0.167, 1, 5, 25, 120),
                      deut_uptake = c(8.003550333, 8.767922333, 9.115434833, 9.705116833, 9.945452833),
                      err_deut_uptake = c(0.0282742947, 0.0556657664, 0.0529310195, 0.0496445668, 0.0794090986),
                      frac_deut_uptake = c(76.85614645, 84.19622478, 87.53330276, 93.19587553, 95.50376366),
                      err_frac_deut_uptake = c(0.383193112, 0.611138265, 0.594304636, 0.5786019863, 0.8332955382),
                      theo_frac_deut_uptake = c(56.35082959, 61.77118851, 64.23548925, 68.41707634, 70.12136088),
                      err_theo_frac_deut_uptake = c(0.2005003133, 0.3947403009, 0.375347506, 0.3520424223, 0.5631103913),
                      theo_deut_uptake = c(7.94652106, 8.71089306, 9.05840556, 9.64808756, 9.88842356),
                      err_theo_deut_uptake = c(0.0282742947, 0.05566576636, 0.05293101952, 0.04964456678, 0.07940909861))

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

states <- unique(dat[["State"]])

########################
## CALCULATE_KINETICS ##
########################

result_tmp <- calculate_kinetics(dat = dat,
                                 protein = chosen_protein,
                                 sequence = chosen_peptide,
                                 state = chosen_state,
                                 start = chosen_peptide_start,
                                 end = chosen_peptide_end,
                                 time_0 = chosen_time_0,
                                 time_100 = chosen_time_100,
                                 deut_part = deut_part)

test_that("data.frame-d calculate_kinetics", expect_s3_class(result_tmp, "data.frame"))

result_tmp <- as.data.table(result_tmp)

lapply(times, function(time){
  
  lapply(deut_values, function(deut_value){
    
    test_name <- paste0("calculate_kinetics-", time, "min-", deut_value)
    
    test_that(test_name,
              expect_equal(
                ref_dat[ref_dat[["Exposure"]] == time, deut_value],
                result_tmp[result_tmp[["Exposure"]] == time, get(deut_value)]
              )
    )
    
  })
  
})


################################
## CALCULATE_PEPTIDE_KINETICS ##
################################

result_tmp <- calculate_peptide_kinetics(dat = dat,
                                         protein = chosen_protein,
                                         sequence = chosen_peptide,
                                         states = states,
                                         start = chosen_peptide_start,
                                         end = chosen_peptide_end,
                                         time_0 = chosen_time_0,
                                         time_100 = chosen_time_100,
                                         deut_part = deut_part)

test_that("data.frame-d calculate_peptide_kinetics", expect_s3_class(result_tmp, "data.frame"))

result_tmp <- as.data.table(result_tmp)

lapply(times, function(time){
  
  lapply(deut_values, function(deut_value){
    
    test_name <- paste0("calculate_peptide_kinetics-", time, "min-", deut_value)
    
    test_that(test_name,
              expect_equal(
                ref_dat[ref_dat[["Exposure"]] == time, deut_value],
                result_tmp[result_tmp[["Exposure"]] == time &
                             result_tmp[["State"]] == chosen_state, get(deut_value)]
              )
    )
    
  })
  
})


############################
## CREATE_KINETIC_DATASET ##
############################

chosen_peptide_list <- dat %>%
  select(Sequence, State, Start, End) %>%
  unique(.)

result_tmp <- create_kinetic_dataset(dat = dat,
                                     peptide_list = chosen_peptide_list,
                                     protein = chosen_protein,
                                     time_0 = chosen_time_0,
                                     time_100 = chosen_time_100,
                                     deut_part = deut_part)

test_that("data.frame-d create_kinetic_dataset", expect_s3_class(result_tmp, "data.frame"))

result_tmp <- as.data.table(result_tmp)

test_that("states in create_kinetic_dataset",
          expect_equal(
            length(unique(result_tmp[["State"]])),
            length(unique(chosen_peptide_list[["State"]]))
          )
)


lapply(times, function(time){
  
  lapply(deut_values, function(deut_value){
    
    test_name <- paste0("create_kinetic_dataset-", time, "min-", deut_value)
    
    test_that(test_name,
              expect_equal(
                ref_dat[ref_dat[["Exposure"]] == time, deut_value],
                result_tmp[result_tmp[["Exposure"]] == time &
                             result_tmp[["State"]] == chosen_state &
                             result_tmp[["Sequence"]] == chosen_peptide, get(deut_value)]
              )
    )
    
  })
  
})

############################
## CALCULATE_STATE_UPTAKE ##
############################

test_that("class is right",
          expect_is(calculate_state_uptake(dat,
                                           protein = chosen_protein,
                                           state = chosen_state,
                                           time_0 = chosen_time_0,
                                           time_t = chosen_time,
                                           time_100 = chosen_time_100),
                    "data.frame"))

lapply(times, function(time){
  
  result_tmp <- calculate_state_uptake(dat,
                                       protein = chosen_protein,
                                       state = chosen_state,
                                       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_state_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)]
              )
    )
    
  })
  
})


#################################
## CREATE_STATE_UPTAKE_DATASET ##
#################################
## chiclet
## butterfly

result_tmp <- create_state_uptake_dataset(dat = dat,
                                          protein = chosen_protein,
                                          state = chosen_state,
                                          time_0 = chosen_time_0,
                                          time_100 = chosen_time_100,
                                          deut_part = deut_part)

test_that("data.frame-d create_state_uptake_dataset", expect_s3_class(result_tmp, "data.frame"))

result_tmp <- as.data.table(result_tmp)

lapply(times, function(time){
  
  lapply(deut_values, function(deut_value){
    
    test_name <- paste0("create_state_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)]
              )
    )
    
  })
  
})


###########################
## CREATE_UPTAKE_DATASET ##
###########################

result_tmp <- create_uptake_dataset(dat = dat,
                                    protein = chosen_protein,
                                    states = unique(dat[["State"]]),
                                    time_0 = chosen_time_0,
                                    time_100 = chosen_time_100,
                                    deut_part = deut_part)

test_that("data.frame-d create_uptake_dataset", expect_s3_class(result_tmp, "data.frame"))

result_tmp <- as.data.table(result_tmp)

lapply(times, function(time){
  
  lapply(deut_values, function(deut_value){
    
    test_name <- paste0("create_uptake_dataset-", time, "min-", deut_value)
    
    test_that(test_name,
              expect_equal(
                ref_dat[ref_dat[["Exposure"]] == time, deut_value],
                result_tmp[result_tmp[["State"]] == chosen_state &
                             result_tmp[["Sequence"]] == chosen_peptide &
                             result_tmp[["Exposure"]] == time, get(deut_value)]
              )
    )
    
  })
  
})


#####################################
## CREATE_STATE_COMPARISON_DATASET ##
#####################################

lapply(times, function(time){
  
  lapply(deut_values, function(deut_value){
    
    result_tmp <- create_state_comparison_dataset(dat = dat,
                                                  protein = chosen_protein,
                                                  states = 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)
    
    test_name <- paste0("create_state_comparison_dataset-", time, "min-", deut_value)
    
    test_that(test_name,
              expect_equal(
                ref_dat[ref_dat[["Exposure"]] == time, deut_value],
                result_tmp[result_tmp[["State"]] == chosen_state &
                             result_tmp[["Sequence"]] == chosen_peptide, get(deut_value)]
              )
    )
    
  })
  
})

# test_that("data.frame-d create_state_comparison_dataset", expect_s3_class(result_tmp, "data.frame"))

############################
## CREATE_CONTROL_DATASET ##
############################

dat_tmp <- create_control_dataset(dat = dat,
                                  control_protein = chosen_protein,
                                  control_state = chosen_state,
                                  control_exposure = chosen_time_100)

test_that("maximal exchange control added",
          expect_true(99999 %in% unique(dat_tmp[["Exposure"]])))


lapply(times, function(time){
  
  result_tmp <- calculate_state_uptake(dat_tmp,
                                       protein = chosen_protein,
                                       state = chosen_state,
                                       time_0 = chosen_time_0,
                                       time_t = time,
                                       time_100 = 99999,
                                       deut_part = deut_part)
  
  result_tmp <- as.data.table(result_tmp)
  
  lapply(deut_values, function(deut_value){
    
    test_name <- paste0("calculate_state_uptake with control -", 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("data.frame-d calculate_state_uptake", expect_s3_class(result_tmp, "data.frame"))