Fix map_snps_to_genes unit test

neurogenomics · Mar 2, 2023 · e19acf1 · e19acf1
1 parent 1c8c2fd
commit e19acf1
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Showing 2 changed files with 4 additions and 100 deletions.
diff --git a/educational_attainment.tsv b/educational_attainment.tsv
diff --git a/tests/testthat/test-map_snps_to_genes.r b/tests/testthat/test-map_snps_to_genes.r
@@ -5,16 +5,14 @@ test_that("map_snps_to_genes works", {
         #### Gather data ####
         ctd <- ewceData::ctd()
         #### Run SNP-to-gene mapping ####
-        ## Use a very small example GWAS file 
-        wd <- getwd()
+        ## Use a very small example GWAS file  
         path_formatted <- MAGMA.Celltyping::get_example_gwas(
-            trait = "educational_attainment",
-            storage_dir = wd)
+            trait = "educational_attainment")
         ## Map
-        genesOutPath <- MAGMA.Celltyping::map_snps_to_genes(
+        genesOutPath <- MAGMA.Celltyping:: map_snps_to_genes(
             path_formatted = path_formatted,
             genome_build = "hg19",
-            N = NULL) 
+            N = 5000) 
         ## Test
         genesOut_cols <- c("GENE","CHR","START","STOP","NSNPS",
                            "NPARAM","N","ZSTAT","P")