tests/testthat/test_loading.R

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

context("load data and annotate")

test_that("load data and annotate", {
  data(OpenSWATH_data, package="SWATH2stats")
  data <- OpenSWATH_data
  data(Study_design, package="SWATH2stats")

  # filter_openSWATH_output
  expect_that(dim(data)[2], equals(58))
  data <- reduce_OpenSWATH_output(data)
  expect_that(dim(data)[2], equals(13))

  # annotate data
  expect_that(dim(data)[2], equals(13))
  data <- sample_annotation(data, Study_design)

  filename.data <- unique(subset(data, Condition == "Hela_Treatment" & BioReplicate == 2 & Run == 4)[,"filename"])
  filename.design <- subset(Study_design, Condition == "Hela_Treatment" & BioReplicate == 2 & Run == 4)[,"Filename"]
  filename.design2 <- subset(Study_design, Condition == "Hela_Treatment" & BioReplicate == 1 & Run == 4)[,"Filename"]

  expect_true(length(grep(filename.design, filename.data))>0)
  expect_error(length(grep(filename.design2, filename.data))>0)
  
  Study_design2 <- Study_design
  Study_design2$Filename <- gsub("(peterb_L[[:digit:]]{6}).*", "\\1", Study_design2$Filename)
  
  # error that it has different number of file names
  expect_error(sample_annotation(data, Study_design2))
  
  # error that the strings in Filename are not unique
  Study_design3 <- Study_design
  Study_design3$Filename <- gsub("peterb_L150514_001_SW", "peterb_L150514", Study_design3$Filename)

  expect_error(sample_annotation(data, Study_design3))
  
  data <- sample_annotation(data, Study_design, verbose = TRUE)
  expect_message(sample_annotation(data, Study_design, verbose = TRUE), "peterb_J131223_043")
  expect_error(sample_annotation(data, Study_design, column_file = "Files"), "Column for filename is not present in data file")
  
  
})

test_that("load MSstats data and annotate", {
  data(MSstats_data, package="SWATH2stats")
  data(Study_design, package="SWATH2stats")
  
  MSstats_data2 <- MSstats_data
  MSstats_data2$mscore <- 0.01
  expect_message(transform_MSstats_OpenSWATH(MSstats_data), "No column 'mscore' present")
  expect_message(transform_MSstats_OpenSWATH(MSstats_data2), "Additional columns present in the data: FileName, mscore")
  
  expect_warning(sample_annotation(MSstats_data[,c(1:6,9:11)], Study_design, data_type = "MSstats", column_file = "FileName"),
                 "The number of sample annotation condition and filenames in data are not balanced")
  
  MSstats_data2$FragmentIon <- NULL
  expect_error(transform_MSstats_OpenSWATH(MSstats_data2), "The data frame doesn't contain all required columns.")
})