inst/tinytest/test_dt.R

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

test_path = system.file("tinytest", "get_dt_test.csv", package = "MSstatsConvert")
test_df = data.table::fread(test_path)

# Import and conversion ----
## data.table from path
expect_equal(class(MSstatsConvert:::.getDataTable(test_path))[1], "data.table")
## data.table from data.frame
expect_equal(class(MSstatsConvert:::.getDataTable(test_df))[1], "data.table")
## When it's not a data.frame, a test 
expect_error(MSstatsConvert:::.getDataTable(numeric(10)))
## Remove unnecessary symbols from column names
expect_equal(MSstatsConvert:::.standardizeColnames("Col.name"), "Colname")
expect_equal(MSstatsConvert:::.standardizeColnames("[Col%name]"), "Colname")
### Does not cover ":" - is it bad?
expect_equal(MSstatsConvert:::.getChannelColumns(c("Ab:1", "Ab:2"), "Ab"), c("Ab:1", "Ab:2"))
# Additional columns
updated_df = MSstatsConvert:::.fillValues(test_df, list(z = NA))
expect_true(all(is.na(updated_df$z)) & is.element("z", colnames(updated_df)))
# Column types ---
updated_col_types = updated_df[, list(x = as.character(x), y = as.factor(y), z = as.numeric(z))]
fixed_column_types = MSstatsConvert:::.fixColumnTypes(updated_col_types, numeric_columns = "x", 
                                                      character_columns = "y",
                                                      factor_columns = "z")
expect_equal(class(fixed_column_types$x), "numeric")
expect_equal(class(fixed_column_types$y), "character")
expect_equal(class(fixed_column_types$z), "factor")