Preparing the data

Prepare your data

• Disease gene list
• Test (hold-out) set of disease genes (optional)
• Any user-provided or already supplied networks (optional)
• Any user-provided or already supplied extra features (optional)

1. Map the genes of all pre-requisites to the index number of each gene provided in the file our_protein_coding_gene_list_20760genes_all_synonyms_genenames_indexed.tsv. The disease gene list has the form of the entire protein coding gene list with 2 columns: (a) the index numbers of genes, and (b) the labels corresponding to the disease gene list (0 for non-included genes, 1 for disease genes).

   See train_node_labels.tsv as example.

   In R:

   Load the protein coding gene list & the disease gene list of interest:

   protein_coding_genes <- read.table("./our_protein_coding_gene_list_20760genes_all_synonyms_genenames_indexed.tsv",
   header=TRUE, dec='.', sep="\t", quote="", stringsAsFactors = FALSE, row.names=NULL)
   Disease_gene_list <- read.table("./target_disease_gene_list.tsv", header=TRUE, dec='.', sep="\t", quote="", stringsAsFactors = FALSE, row.names=NULL)

   Match the indexing of the protein coding gene list to the genes in your disease gene list of target (gene names have to be in HGCN (“Gene” column) or Ensemble (“Gene_ID” column) format), remove rows of genes that were not matched, and keep only the column of the indexed nodes:

   Disease_gene_list$node <- protein_coding_genes$index[match(Disease_gene_list $Gene,protein_coding_genes$Gene)]
   Disease_gene_list <- Disease_gene_list[complete.cases(Disease_gene_list$Gene),]
   Disease_gene_list[c("Gene_ID","Gene",)])] <- NULL

2. Repeat mapping for the test (hold-out) set when applicable.

3. Repeat for the networks. For user-provided networks that are in the form of 3 columns: Gene1, Gene2, weight. Supplied networks are prepared and ready to be used. Load your networks as above and match indexed genes to the 2 gene columns, set column names as “src”, “dst”, “weight”, and remove signed weights. Keep only rows where gene names have an index number.

   Network1$src <- protein_coding_genes$index[match(Network1$Gene1,protein_coding_genes$Gene)] 
   Network1$dst <- protein_coding_genes$index[match(Network1$Gene2,protein_coding_genes$Gene)]  
   Network1[c("Gene1", "Gene2")] <- NULL
   names(Network1)<- c("weight", "src", "dst")
   Network1<- Network1[,c(2,3,1)] 
   Network1['weight'] <- gsub("^-","",Network1$weight)
   Network1<- Network1 [complete.cases(Network1), ]