inst/unitTests/test_w4m2bioc.R

In ethevenot/r-w4m2bioc: Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class

test_readw4m <- function() {

    sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
    library(Biobase)

}

test_dataMatrix_get <- function() {

    sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
    library(Biobase)
    checkEqualsNumeric(exprs(sacSet)["Tryptophan", "HU_020"], 4.594285, tol = 1e-6)

}

test_sampleMetadata_get <- function() {

    sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
    library(Biobase)
    checkEqualsNumeric(pData(sacSet)["HU_017", "bmi"], 23.03, tol = 1e-2)

}

test_variableMetadata_get <- function() {

    sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
    library(Biobase)
    checkEquals(fData(sacSet)["Taurine", "hmdb"], "HMDB00251")

}

test_sampleNames_get <- function() {

    sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
    library(Biobase)
    checkEquals(sampleNames(sacSet)[3], "HU_015")

}

test_variableNames_get <- function() {

    sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
    library(Biobase)
    checkEquals(featureNames(sacSet)[5], "X1.3.Dimethyluric.acid")

}