From 7492de9be6c1a1de18f0c87cd184f0491f2ea240 Mon Sep 17 00:00:00 2001
From: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Date: Mon, 5 May 2025 19:08:37 -0400
Subject: [PATCH] added unit test for duplicate filtering

---
 R/NetworkDataCompanion.R                      | 17 +++++++--------
 ...t_filterDuplicatesMethylationMissingness.R | 21 +++++++++++++++++++
 .../testdata/duplicate_meth_uuids.csv         |  6 ++++++
 3 files changed, 34 insertions(+), 10 deletions(-)
 create mode 100644 tests/testthat/test_filterDuplicatesMethylationMissingness.R
 create mode 100644 tests/testthat/testdata/duplicate_meth_uuids.csv

diff --git a/R/NetworkDataCompanion.R b/R/NetworkDataCompanion.R
index fc56b9a..dfa8340 100644
--- a/R/NetworkDataCompanion.R
+++ b/R/NetworkDataCompanion.R
@@ -521,17 +521,14 @@ NetworkDataCompanion=setRefClass("NetworkDataCompanion",
              missing_df = data.frame("uuid"=names(methylation_betas[,-1]),
                                      "prop_miss"=apply(methylation_betas[,-1],2,
                                                        function(x){sum(is.na(x))/length(x)}))
-             tcga_barcodes = ndc$mapUUIDtoTCGA(missing_df$uuid)
-             keep_barcodes = missing_df %>% inner_join(tcga_barcodes, by=c("uuid"="file_id")) %>%
-               dplyr::rename("TCGA_barcode"=submitter_id) %>% 
-               mutate(TCGA_sample_and_type =  ndc$extractSampleAndType(TCGA_barcode)) %>%
+             tcga_barcodes = mapUUIDtoTCGA(missing_df$uuid)
+             missing_df %>% inner_join(tcga_barcodes, by=c("uuid"="file_id")) %>%
+               dplyr::rename("TCGA_barcode" = submitter_id) %>% 
+               mutate(TCGA_sample_and_type = extractSampleAndType(TCGA_barcode)) %>%
                group_by(TCGA_sample_and_type) %>%
-               summarize("TCGA_barcode_min_prop_miss"=TCGA_barcode[which.min(prop_miss)]) %>%
-               pull(TCGA_barcode_min_prop_miss) 
-             
-             keep_uuids = tcga_barcodes %>% dplyr::filter(submitter_id %in% keep_barcodes) %>%
-               pull(file_id)
-             return(keep_uuids)
+               summarize("uuid_min_prop_miss"=uuid[which.min(prop_miss)]) %>%
+               pull(uuid_min_prop_miss) %>%
+               return()
            },
            
            ## Filter samples indicated by *TCGA_barcodes* based on the method *method* and threshold *threshold*
diff --git a/tests/testthat/test_filterDuplicatesMethylationMissingness.R b/tests/testthat/test_filterDuplicatesMethylationMissingness.R
new file mode 100644
index 0000000..d428d22
--- /dev/null
+++ b/tests/testthat/test_filterDuplicatesMethylationMissingness.R
@@ -0,0 +1,21 @@
+context("[NetworkDataCompanion] Testing filterDuplicatesMethylationMissingness function ... ")
+
+test_that("Testing filterDuplicatesMethylationMissingness",{
+  # samples loaded from quickstart, Harvard dataverse archive
+  # data_download/methylation/tcga_coad_cms1_methylations.txt
+  id_map = read.csv("testdata/duplicate_meth_uuids.csv", row.names=1)
+  # fake methylation data with various missingness
+  beta_vals = matrix(nrow=3,ncol=6)
+  beta_vals[,3] = rep(1,3) # this should be picked
+  beta_vals[,4] = c(NA,rep(1,2))
+  beta_vals[,5] = rep(1,3) 
+  beta_df = data.frame(beta_vals)
+  beta_df[,1] = c("cg00000001",
+                  "cg00000002",
+                  "cg00000003")
+  names(beta_df) =c("probeID",id_map$file_id)
+  
+  my_friend = NetworkDataCompanion::CreateNetworkDataCompanionObject()
+  keep_uuids = my_friend$filterDuplicatesMethylationMissingness(beta_df)
+  expect_equal(keep_uuids, c(id_map$file_id[2],id_map$file_id[4]))
+})
diff --git a/tests/testthat/testdata/duplicate_meth_uuids.csv b/tests/testthat/testdata/duplicate_meth_uuids.csv
new file mode 100644
index 0000000..ab69d85
--- /dev/null
+++ b/tests/testthat/testdata/duplicate_meth_uuids.csv
@@ -0,0 +1,6 @@
+"","file_id","submitter_id"
+"ff44ff4e-15e9-46b6-986d-484dfd08bb16","ff44ff4e-15e9-46b6-986d-484dfd08bb16","TCGA-A6-6780-01A"
+"6852b9a2-de41-45a4-a63b-a4a415b5cac4","6852b9a2-de41-45a4-a63b-a4a415b5cac4","TCGA-A6-3809-01A"
+"8b6e4521-ed23-4ddd-96a4-941d36065418","8b6e4521-ed23-4ddd-96a4-941d36065418","TCGA-A6-3809-01B"
+"d0730cce-7c73-4125-9022-5dc1069920b6","d0730cce-7c73-4125-9022-5dc1069920b6","TCGA-A6-6780-01A"
+"391664d3-d617-4b6f-9d81-78cf83f61520","391664d3-d617-4b6f-9d81-78cf83f61520","TCGA-A6-6780-01B"