UM-Applied-Algorithms-Lab · Gram-S · Jun 17, 2026 · Jun 17, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,6 +38,7 @@ Depends:
     R (>= 4.5.0)
 URL: https://um-applied-algorithms-lab.github.io/PTMsToPathways/
 BugReports: https://github.com/UM-Applied-Algorithms-Lab/PTMsToPathways/issues/new
+LazyData: true
 Config/testthat/edition: 3
 Additional_repositories: https://bioconductor.org/packages/3.21/bioc
 biocViews: Software, Proteomics, PostTranslationalModifications, Pathways, Network
diff --git a/man/BRCA_PCN.data.Rd b/man/BRCA_PCN.data.Rd
diff --git a/man/BRCA_genemania.edges.Rd b/man/BRCA_genemania.edges.Rd
diff --git a/man/BRCA_stringdb.edges.Rd b/man/BRCA_stringdb.edges.Rd
diff --git a/man/brca_CCCN_data.Rd b/man/brca_CCCN_data.Rd
diff --git a/man/brca_clusterlist_data.Rd b/man/brca_clusterlist_data.Rd
diff --git a/man/ex_PCNedgelist.Rd b/man/ex_PCNedgelist.Rd
diff --git a/man/ex_adj_consensus.Rd b/man/ex_adj_consensus.Rd
diff --git a/man/ex_bioplanet.Rd b/man/ex_bioplanet.Rd
diff --git a/man/ex_cfn.Rd b/man/ex_cfn.Rd
diff --git a/man/ex_combined_ppi.Rd b/man/ex_combined_ppi.Rd
diff --git a/man/ex_common_clusters.Rd b/man/ex_common_clusters.Rd
diff --git a/man/ex_full_ptm_table.Rd b/man/ex_full_ptm_table.Rd
diff --git a/man/ex_gene_cccn_edges.Rd b/man/ex_gene_cccn_edges.Rd
diff --git a/man/ex_gene_cccn_nodes.Rd b/man/ex_gene_cccn_nodes.Rd
diff --git a/man/ex_genemania_edges.Rd b/man/ex_genemania_edges.Rd
diff --git a/man/ex_pathway_crosstalk_network.Rd b/man/ex_pathway_crosstalk_network.Rd
diff --git a/man/ex_pathways_list.Rd b/man/ex_pathways_list.Rd
diff --git a/man/ex_ptm_cccn_edges.Rd b/man/ex_ptm_cccn_edges.Rd
diff --git a/man/ex_ptm_correlation_matrix.Rd b/man/ex_ptm_correlation_matrix.Rd
diff --git a/man/ex_small_ptm_table.Rd b/man/ex_small_ptm_table.Rd
diff --git a/man/ex_stringdb_edges.Rd b/man/ex_stringdb_edges.Rd
diff --git a/man/ex_tiny_ptm_table.Rd b/man/ex_tiny_ptm_table.Rd
diff --git a/man/function_key.Rd b/man/function_key.Rd
diff --git a/tests/testthat/test_buildclusterfilterednetwork.R b/tests/testthat/test_buildclusterfilterednetwork.R
@@ -2,12 +2,12 @@
 
 test_that("BuildClusterFilteredNetwork() gives right answer", {
 
-  # Get example data
+  # Run the function to test
+
   gene_cccn_edges <- PTMsToPathways::ex_gene_cccn_edges
   stringdb_edges <- PTMsToPathways::ex_stringdb_edges
   genemania_edges <- PTMsToPathways::ex_genemania_edges
-
-  # Run the function to test
+
   output <- BuildClusterFilteredNetwork(gene_cccn_edges, stringdb_edges, genemania_edges, NULL)
 
   # Test the combined PPI output

diff --git a/tests/testthat/test_buildpathwaycrosstalknetwork.R b/tests/testthat/test_buildpathwaycrosstalknetwork.R
@@ -1,13 +1,8 @@
 # THESE USE DATA GENERATED FROM THE SMALL PTM TABLE 
 
-# Get data from package
-common_clusters <- PTMsToPathways::ex_common_clusters
-pathways_list <- PTMsToPathways::ex_pathways_list
-
-
 test_that("BuildPathwayCrosstalkNetwork() gives right answer", {
-
-  output <- suppressMessages(BuildPathwayCrosstalkNetwork(common_clusters, pathways_list, createfile = FALSE))
+  
+  output <- suppressMessages(BuildPathwayCrosstalkNetwork(ex_common_clusters, ex_pathways_list, createfile = FALSE))
 
   pathway_crosstalk_network <- output[[1]]
 
@@ -53,9 +48,9 @@ test_that("BuildPathwayCrosstalkNetwork() gives right answer", {
 test_that("ReadBioplanetFile() gives right answer", {
   # read pathways.csv from inst/extdata and compare to ex_pathways_list
   bioplanet_pathways <- ReadBioplanetFile(system.file("extdata", "pathway.csv", package = "PTMsToPathways"))
-  expect_equal(length(bioplanet_pathways), length(pathways_list))
-  for (pathway_name in names(pathways_list)) {
+  expect_equal(length(bioplanet_pathways), length(ex_pathways_list))
+  for (pathway_name in names(ex_pathways_list)) {
     expect_true(pathway_name %in% names(bioplanet_pathways))
-    expect_equal(sort(bioplanet_pathways[[pathway_name]]), sort(pathways_list[[pathway_name]]))
+    expect_equal(sort(bioplanet_pathways[[pathway_name]]), sort(ex_pathways_list[[pathway_name]]))
   }
 })
diff --git a/tests/testthat/test_gatherppidata.R b/tests/testthat/test_gatherppidata.R
@@ -1,13 +1,9 @@
 # THESE USE DATA GENERATED FROM THE SMALL PTM TABLE 
 
-# Get data from package
-gene_cccn_edges <- PTMsToPathways::ex_gene_cccn_edges
-gene_cccn_nodes <- PTMsToPathways::ex_gene_cccn_nodes
-
 test_that("GetGeneMANIA.edges() gives right answer", {
 
   path <- system.file('extdata/ex_genemania_interactions.txt', package='PTMsToPathways') # Accesses the path to this file even run on github or devtools::test
-  genemania_edges <- GetGeneMANIA.edges(path, gene_cccn_nodes) # Run function and filter data
+  genemania_edges <- GetGeneMANIA.edges(path, ex_gene_cccn_nodes) # Run function and filter data
   col_1 <- as.list(genemania_edges[,1])
   row_2 <- as.list(genemania_edges[2,])
 
@@ -23,7 +19,7 @@ test_that("GetGeneMANIA.edges() gives right answer", {
 test_that("GetSTRINGdb.edges() gives right answer with local file", {
 
   path <- system.file('extdata/small_string_hs_hugo.tsv', package='PTMsToPathways')
-  stringdb_edges <- suppressMessages(GetSTRINGdb.edges(gene_cccn_edges, gene_cccn_nodes, local = TRUE, string.local.path = path))
+  stringdb_edges <- suppressMessages(GetSTRINGdb.edges(ex_gene_cccn_edges, ex_gene_cccn_nodes, local = TRUE, string.local.path = path))
 
   # Expected values
   exp_row_100 <- data.frame(source = "PLEKHA7", target = "EPB41L2", interaction = "experimental", Weight = 292) 
@@ -36,7 +32,7 @@ test_that("GetSTRINGdb.edges() gives right answer with local file", {
 test_that("GetKinsub.edges() gives right answer", {
 
   path <- system.file('extdata/Kinase_Substrate_Dataset.txt', package='PTMsToPathways')
-  kinsub_edges <- GetKinsub.edges(path, gene_cccn_nodes)
+  kinsub_edges <- GetKinsub.edges(path, ex_gene_cccn_nodes)
 
   # Expected values
   exp_row_1 <- data.frame(source = "EGFR", target = "PLCG1", interaction = "pp", Weight = 1) 

diff --git a/tests/testthat/test_makeclusterlist.R b/tests/testthat/test_makeclusterlist.R
@@ -7,8 +7,7 @@ test_that("MakeClusterList() gives right answer", {
     clust1 <- list("RACK1 p T229", "ATP6V1H p Y388", "TNK2 p T829", "IRS2 p Y632")
     clust2 <- list("EIF2S1 p Y147", "ACTG1 p T297; ACTB p T297", "PDLIM5 p T248", "LSR p S365", "DCP1A p Y64", "MAPK13 p T185", "ALK p S1509", "GAREM1 p S700")
 
-    # Get data from package
-    ptmtable <- PTMsToPathways::ex_tiny_ptm_table
+    ptmtable <- ex_tiny_ptm_table
 
     clusterlist_data <- suppressMessages(MakeClusterList(ptmtable, keeplength = 2, toolong = 3.5))
     common_clusters <- clusterlist_data[[1]]

diff --git a/tests/testthat/test_makecorrelationnetwork.R b/tests/testthat/test_makecorrelationnetwork.R
@@ -2,12 +2,8 @@
 
 test_that("MakeCorrelationNetwork() gives right answer", {
 
-    # Get data from package
-    adj_consensus <- PTMsToPathways::ex_adj_consensus
-    ptm_correlation_matrix <- PTMsToPathways::ex_ptm_correlation_matrix
-
-    # Run the function and get results
-    correlationnetwork_data <- suppressMessages(MakeCorrelationNetwork(adj_consensus, ptm_correlation_matrix))
+    # now run MakeCorrelationNetwork
+    correlationnetwork_data <- suppressMessages(MakeCorrelationNetwork(ex_adj_consensus, ex_ptm_correlation_matrix))
     ptm_cccn_edges <- correlationnetwork_data[[1]]
     gene_cccn_edges <- correlationnetwork_data[[2]]
     gene_cccn_nodes <- correlationnetwork_data[[3]]

diff --git a/vignettes/BRCANetworks.Rmd b/vignettes/BRCANetworks.Rmd
@@ -61,8 +61,6 @@ available:
 
 ```{r eval = TRUE}
 library(PTMsToPathways)
-data_names <- data(package = "PTMsToPathways")$results[, "Item"]
-data(list = data_names, package = "PTMsToPathways")
 ```
 
 ### Preprocess data for PTMsToPathways functions

diff --git a/vignettes/CreatingNetworks.Rmd b/vignettes/CreatingNetworks.Rmd
@@ -71,8 +71,6 @@ And load the package:
 
 ```{r eval = TRUE, echo = TRUE}
 library(PTMsToPathways)
-data_names <- data(package = "PTMsToPathways")$results[, "Item"]
-data(list = data_names, package = "PTMsToPathways")
 ```
 
 # Starting Data

diff --git a/vignettes/CytoscapeGraphing.Rmd b/vignettes/CytoscapeGraphing.Rmd
@@ -58,9 +58,6 @@ built-in P2P function [ReadBioplanetFile()](reference/ReadBioplanetFile.html).
 
 ```{r eval = TRUE, echo = FALSE}
 library(PTMsToPathways)
-data_names <- data(package = "PTMsToPathways")$results[, "Item"]
-data(list = data_names, package = "PTMsToPathways")
-funckey <- function_key
 pathways.list <- ReadBioplanetFile(system.file("extdata", "bioplanet_pathway_June2025.csv", package = "PTMsToPathways"))
 ```
 

diff --git a/vignettes/RawDataProcessing.Rmd b/vignettes/RawDataProcessing.Rmd
@@ -72,8 +72,6 @@ data will dictate the names of modifications.
 First, let's load the P2P package, since it contains some helpful pre-processing functions.
 ```{r eval = TRUE}
 library(PTMsToPathways)
-data_names <- data(package = "PTMsToPathways")$results[, "Item"]
-data(list = data_names, package = "PTMsToPathways")
 ```
 
 The example raw data file for this