fix unit tests

neurogenomics · Jul 15, 2023 · c773cbe · c773cbe
1 parent 6daff7d
commit c773cbe
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Showing 7 changed files with 9 additions and 7 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -2,8 +2,10 @@
 
 ## Bug fixes
 
-- `create_fake_gwas_path`
+* `create_fake_gwas_path`
   - Don't remove "MAGMA_Files" from all parts of path.
+* `magma_files_metadata`
+  - Update metadata. 
 
 # MAGMA.Celltyping 2.0.10
 

diff --git a/R/calculate_conditional_celltype_enrichment_limma.R b/R/calculate_conditional_celltype_enrichment_limma.R
@@ -28,7 +28,7 @@
 #' 
 #' #### MAGMA 2 #####
 #' genesOut2 <- MAGMA.Celltyping::import_magma_files(
-#'     ids = c("ukb-b-6548"),
+#'     ids = c("ukb-a-333"),
 #'     file_types = ".genes.out",
 #'     return_dir = FALSE)
 #' magma2 <- MAGMA.Celltyping::adjust_zstat_in_genesOut(

diff --git a/R/import_magma_files_metadata.R b/R/import_magma_files_metadata.R
@@ -17,7 +17,7 @@
 import_magma_files_metadata <- function(file_types,
                                         use_local = TRUE,
                                         verbose = TRUE){
-    if(use_local){
+    if(isTRUE(use_local)){
         magma_files_metadata <- MAGMA.Celltyping::magma_files_metadata
     } else{
         magma_files_metadata <- data.table::fread(
@@ -37,5 +37,5 @@ import_magma_files_metadata <- function(file_types,
     #     query = paste(file_types, collapse = "|"),
     #     return_download_api = TRUE,
     #     verbose = verbose
-    # ) 
+    # )
 }
diff --git a/data/magma_files_metadata.rda b/data/magma_files_metadata.rda
diff --git a/man/calculate_conditional_celltype_enrichment_limma.Rd b/man/calculate_conditional_celltype_enrichment_limma.Rd
diff --git a/man/magma_files_metadata.Rd b/man/magma_files_metadata.Rd
diff --git a/tests/testthat/test-calculate_conditional_celltype_enrichment_limma.R b/tests/testthat/test-calculate_conditional_celltype_enrichment_limma.R
@@ -27,7 +27,7 @@ test_that("calculate_conditional_celltype_enrichment_limma works", {
 
         #### MAGMA 2 #####
         genesOut2 <- MAGMA.Celltyping::import_magma_files(
-            ids = c("ukb-b-6548"),
+            ids = c("ukb-a-333"),
             file_types = ".genes.out",
             return_dir = FALSE)
         magma2 <- MAGMA.Celltyping::adjust_zstat_in_genesOut(