Merge branch 'master' of https://git-r3lab.uni.lu/david.hoksza/bh19-rare-diseases

associations/extend_network/get_extended_network.R

@@ -58,6 +58,11 @@ retrieve_stringdb_net <- function(finput, fn, fscore) {
   entities <- paste0("9606.", ensprotein_idest$ensembl_peptide_id)
   entities <- paste(entities, collapse = "%0A" )
   
+  resp <- httr::POST(url = "api.jensenlab.org/network",
+                     httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"),
+                     body = paste0("entities=", entities, "&additional=", n),
+                     httr::verbose())
+  
   json <- jsonlite::fromJSON(httr::content(resp, as = "text", encoding = "UTF-8"), flatten = FALSE)
   
   ### May be important for later, when node-level info can be used for filtering
@@ -179,74 +184,4 @@ if(nrow(ppi_network) == 0) {
                                 "is_directed", "consensus_direction", "references")]
   
   write.table(ppi_network, outputFile, sep = "\t", quote = F, row.names = F, col.names = T)
-}
-
-#   gene_info_2entrez <- subset(gene_info_2entrez, entrezgene_id != "")
-#   
-#   result <- merge(result, gene_info_2entrez, by.x = "source_hgnc_symbol", by.y = "hgnc_symbol" ) 
-#   colnames(result)[which(names(result) == "entrezgene_id")] <- "source_entrezgene_id"
-#   result <- merge(result, gene_info_2entrez, by.x = "target_hgnc_symbol", by.y = "hgnc_symbol" ) 
-#   colnames(result)[which(names(result) == "entrezgene_id")] <- "target_entrezgene_id"
-#   
-#   result$pair <-apply(result,1,function(x){paste(sort(x[c("source_hgnc_symbol","target_hgnc_symbol")]),collapse=":")})
-#   ppi_network$pair <-apply(ppi_network,1,function(x){paste(sort(x[c("source_hgnc_symbol","target_hgnc_symbol")]),collapse=":")})
-#   
-#   message(paste0("from ",length(unique(ppi_network$pair))," pairs of interacting proteins from stringdb"))
-#   message(paste0("we found ", length(intersect(ppi_network$pair, result$pair) ), " interacting pairs in Omnipath"))
-#   
-#   final_results <- unique(subset(result, pair %in% ppi_network$pair)[c( "source_hgnc_symbol","source_entrezgene_id",
-#                                                                         "target_hgnc_symbol", "target_entrezgene_id",
-#                                                                         "is_directed", "consensus_direction", "references", "pair" )])
-#   ppi_network <- subset(ppi_network, !pair %in% final_results$pair)
-#   ppi_network <- within(ppi_network , rm(score, pair))
-#   
-#   final_results <- merge( final_results[, -grep("pair", colnames(final_results))], 
-#                           ppi_network, all = T    )
-#   final_results$is_directed <- ifelse(is.na(final_results$is_directed), 0, as.character(final_results$is_directed))
-#   
-#   message(paste0(" And from those ",dim(subset(final_results, is_directed == 1) )[1], " interacting pairs have direction in Omnipath"))
-#   
-#   if( nrow( final_results ) == 0 ){
-#     warning("None of the pairs of interacting proteins havee pased the filters") 
-#   } else {
-#     write.table(final_results, outputFile, sep = "\t", quote = F, row.names = F)
-#   }
-# } else {
-#   message("Retrieving data from Omnipath")
-#   
-#   url <- paste0("http://omnipathdb.org/interactions/?genesymbols=1&partners=", paste(input, collapse = ","), "&fields=sources,references")
-#   dataTsv <- RCurl::getURLContent( url     )
-#   myTextConnection <- textConnection( dataTsv )
-#   result <- read.csv( myTextConnection, header = TRUE, sep = "\t", colClasses=c("character"))
-#   
-#   colnames(result)[which(names(result) == "source_genesymbol")] <- "source_hgnc_symbol"
-#   colnames(result)[which(names(result) == "target_genesymbol")] <- "target_hgnc_symbol"
-#   result$pair <-apply(result,1,function(x){paste(sort(x[c("source_hgnc_symbol","target_hgnc_symbol")]),collapse=":")})
-#   message(paste0("there are ",length(unique(result$pair))," pairs of interacting proteins from omnipath"))
-#   ensembl <- useMart("ensembl")
-#   ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
-#   
-#   gene_info_2entrez <- getBM(attributes=c('hgnc_symbol', 'entrezgene_id'), 
-#                              filters = 'hgnc_symbol', 
-#                              values = c(result$source_hgnc_symbol, result$target_hgnc_symbol), 
-#                              mart = ensembl)
-#   gene_info_2entrez <- subset(gene_info_2entrez, entrezgene_id != "")
-#   
-#   result <- merge(result, gene_info_2entrez, by.x = "source_hgnc_symbol", by.y = "hgnc_symbol" ) 
-#   colnames(result)[which(names(result) == "entrezgene_id")] <- "source_entrezgene_id"
-#   result <- merge(result, gene_info_2entrez, by.x = "target_hgnc_symbol", by.y = "hgnc_symbol" ) 
-#   colnames(result)[which(names(result) == "entrezgene_id")] <- "target_entrezgene_id"
-#   
-#   
-#   result <- unique(result[c( "source_hgnc_symbol", "source_entrezgene_id",
-#                              "target_hgnc_symbol", "target_entrezgene_id",
-#                              "is_directed", "consensus_direction", "references"  )])
-#   
-#   
-#   if( nrow( result ) == 0 ){
-#     warning("None of the pairs of interacting proteins have pased the filters") 
-#   } else {
-#     write.table(result, outputFile, sep = "\t", quote = F, row.names = F)
-#   }
-#   
-# }
+}
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