Skip to content

Fix devtools check stuff #23

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
lgw2 merged 3 commits into from
Jun 22, 2026
Merged

Fix devtools check stuff #23

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
87aab07
call read.table explicitly from utils
lgw2 Jun 22, 2026
c0ebb9d
remove variable that is never used
lgw2 Jun 22, 2026
138d48a
remove .data
lgw2 Jun 22, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions R/GatherPPIData.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down
4 changes: 2 additions & 2 deletions R/MakeClusterList.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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),
Expand All @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion R/MakeCorrelationNetwork.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
Loading