tests/testthat/test-create_top10percent_genesets_file.r

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

test_that("create_top10percent_genesets_file works", {
    
    if(!is_32bit()){
        ctd <- ewceData::ctd()
        annotLevel <- 1
        #### Prepare GWAS MAGMA data ####
        myGenesOut <- MAGMA.Celltyping::import_magma_files(
            ids = "ieu-a-298",
            file_types = ".genes.out",
            return_dir = FALSE)
        ctd <- MAGMA.Celltyping::prepare_quantile_groups(ctd = ctd)
        geneSetsFilePath <- MAGMA.Celltyping:::create_top10percent_genesets_file(
            genesOutFile = myGenesOut,
            ctd = ctd,
            annotLevel = annotLevel,
            ## Mapped to human orths by prepare_quantile_groups previously
            ctd_species = "human"
        )
        geneSets <- readLines(geneSetsFilePath)
        #### One line per cell-type ####
        testthat::expect_equal(
            length(geneSets),
            ncol(ctd[[annotLevel]]$mean_exp)
        )
        #### That cell-type names are recoverable #### 
        celltypes <- unlist(lapply(geneSets, function(x) {
            strsplit(x, " ")[[1]][1]
        }))
        testthat::expect_true(
            all(celltypes %in% EWCE::fix_celltype_names(colnames(ctd[[annotLevel]]$mean_exp)))
        ) 
    } else {
        testthat::expect_null(NULL)
    }
})