small clean up

EvolEcolGroup · Apr 22, 2024 · 87948f6 · 87948f6
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commit 87948f6
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Showing 4 changed files with 4 additions and 17 deletions.
diff --git a/R/gen_tibble.R b/R/gen_tibble.R
@@ -357,14 +357,8 @@ check_allele_alphabet <- function(x,
 
 }
 
-# make all missing value equal to 0
+# set all missing values to NA
 # loci_info is usually from show_loci()
-#harmonise_missing_values <- function (loci_info, missing_alleles =c("0",".")){
-#  loci_info$allele_ref[loci_info$allele_ref %in% missing_alleles]<-"0"
-#  loci_info$allele_alt[loci_info$allele_alt %in% missing_alleles]<-"0"
-#  return(loci_info)
-#}
-
 harmonise_missing_values <- function (loci_info, missing_alleles =c("0",".")){
   # 0 is always considered as a missing value
   if ("0" %in% missing_alleles){

diff --git a/tests/testthat/test_gen_tibble.R b/tests/testthat/test_gen_tibble.R
@@ -16,9 +16,6 @@ bed_path <- gt_write_bed_from_dfs(genotypes = test_genotypes,
                                   path_out = tempfile('test_data_'))
 test_gt <- gen_tibble(bed_path, quiet = TRUE)
 
-# we now replace NA with 0 for the test_loci
-#test_loci[is.na(test_loci)]<-"0"
-
 # this also tests show_genotypes and show_loci
 test_that("create gen_tibble from bed",{
   expect_true(inherits(test_gt,"gen_tbl"))

diff --git a/tests/testthat/test_gen_tibble_save_load.R b/tests/testthat/test_gen_tibble_save_load.R
@@ -16,9 +16,6 @@ bed_path <- gt_write_bed_from_dfs(genotypes = test_genotypes,
                                   path_out = tempfile('test_data_'))
 test_gt <- gen_tibble(bed_path, quiet = TRUE)
 
-# we now replace NA with 0 for the test_loci
-#test_loci[is.na(test_loci)]<-"0"
-
 # this also tests show_genotypes and show_loci
 test_that("save and load gt",{
   expect_true(inherits(test_gt,"gen_tbl"))
@@ -43,9 +40,12 @@ test_that("save and load gt",{
   expect_true(file.copy(from=all_file_names[3],
                         to=file.path(new_dir, basename(all_file_names[3]))))
   expect_true(file.remove(all_file_names[2]))
+
   #expect_true(file.remove(all_file_names[3]))
   #TODO the above test fails on Windows,
   #needs a fix after response to bistatsr issue
+
+
   # loading should fail
   expect_error(new_test_gt2 <- gt_load(all_file_names[1]))
   # this should now work:

diff --git a/tests/testthat/test_show_loci.R b/tests/testthat/test_show_loci.R
@@ -16,10 +16,6 @@ test_that("show_loci gets and sets information",{
                                     path_out = tempfile('test_data_'))
   test_gt <- gen_tibble(bed_path, quiet = TRUE)
 
-  # we now replace NA with 0 for the test_loci
-  #test_loci[is.na(test_loci)]<-"0"
-
-
   # check that we retrieve the info we put in (as a tibble)
   expect_identical(show_loci(test_gt) %>% select(-big_index),as_tibble(test_loci))
   # now change it directly on the genotype column