From 87aab072112ae994735c0092838be6d3ba7f6d51 Mon Sep 17 00:00:00 2001 From: Lucy Date: Mon, 22 Jun 2026 16:39:39 -0600 Subject: [PATCH 1/3] call read.table explicitly from utils --- R/GatherPPIData.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/GatherPPIData.R b/R/GatherPPIData.R index 54d4f131..27819364 100644 --- a/R/GatherPPIData.R +++ b/R/GatherPPIData.R @@ -498,7 +498,7 @@ GetGeneMANIA.edges <- function(gm.results.path, network_lines <- all_lines[start_line[1]:(end_line[1] - 1)] - edgetable <- read.table( + edgetable <- utils::read.table( text = network_lines, header = TRUE, stringsAsFactors = FALSE, @@ -552,7 +552,7 @@ GetKinsub.edges <- function(kinasesubstrate.filename = "Kinase_Substrate_Dataset symbol.map = NULL) { nodes <- toupper(.map_nodes_with_symbol_map(gene.cccn.nodes, symbol.map)) - kinasesubstrateraw <- read.table( + kinasesubstrateraw <- utils::read.table( kinasesubstrate.filename, header = TRUE, skip = 3, From c0ebb9d6e5a99bef06f03af714ab270d029a15bc Mon Sep 17 00:00:00 2001 From: Lucy Date: Mon, 22 Jun 2026 16:46:46 -0600 Subject: [PATCH 2/3] remove variable that is never used --- R/MakeClusterList.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/MakeClusterList.R b/R/MakeClusterList.R index 9a425876..ef96cab1 100644 --- a/R/MakeClusterList.R +++ b/R/MakeClusterList.R @@ -138,7 +138,7 @@ MakeClusterList <- function(ptmtable, keeplength = 2, toolong = 3.5, tsne_perple # 2. For each cluster, set all PTM–PTM pairs in the cluster to 1 (indicating co-membership). # 3. The final matrix for a method has 1 for PTM pairs co-clustered in that method; 0 otherwise. - co_membership_matrix <- function(clusters, all_ptms) { + co_membership_matrix <- function(clusters) { # 1. square matrix of all PTMs mat <- matrix(0, nrow = length(PTMnames), ncol = length(PTMnames), @@ -155,7 +155,7 @@ MakeClusterList <- function(ptmtable, keeplength = 2, toolong = 3.5, tsne_perple return(mat) } - adjacency_matrices <- purrr::map(clusters.list, co_membership_matrix, all_ptms = all_ptms) + adjacency_matrices <- purrr::map(clusters.list, co_membership_matrix) # Step 2: Sum the Co-Membership Matrices Across Methods adj.sum <- Reduce("+", adjacency_matrices) # values: 0 (never), 1, 2, 3 (co-clustered in all 3 methods) From 138d48a3ed297e15a7d28a09078fbf37b512f3cb Mon Sep 17 00:00:00 2001 From: Lucy Date: Mon, 22 Jun 2026 16:51:40 -0600 Subject: [PATCH 3/3] remove .data --- R/MakeCorrelationNetwork.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/MakeCorrelationNetwork.R b/R/MakeCorrelationNetwork.R index aade533e..db3301c3 100644 --- a/R/MakeCorrelationNetwork.R +++ b/R/MakeCorrelationNetwork.R @@ -87,7 +87,7 @@ MakeCorrelationNetwork <- function(adj.consensus.matrix, ptm.correlation.matrix) # Sum correlations in one dimension, then the other dimension gene.cccn2 <- dplyr::summarise( - dplyr::group_by(gene.cccn, .data$Gene.Name), + dplyr::group_by(gene.cccn, Gene.Name), dplyr::across( tidyselect::where(is.numeric), ~ sum(.x, na.rm = TRUE)