inst/doc/buildingPPIsFromStringDB.R

In netSmooth: Network smoothing for scRNAseq

## ---- echo=TRUE,eval=FALSE----------------------------------------------------
#  require(STRINGdb)
#  require(igraph)
#  require(biomaRt)
#  
#  # 1. getSTRINGdb for human
#  string_db <- STRINGdb$new(species=9606)
#  human_graph <- string_db$get_graph()
#  
#  # 2. get edges with high confidence score
#  edge.scores <- E(human_graph)$combined_score
#  ninetyth.percentile <- quantile(edge.scores, 0.9)
#  thresh <- data.frame(name='90th percentile',
#                       val=ninetyth.percentile)
#  human_graph <- subgraph.edges(human_graph,
#                                E(human_graph)[combined_score > ninetyth.percentile])
#  
#  # 3. create adjacency matrix
#  adj_matrix <- as_adjacency_matrix(human_graph)
#  
#  
#  # 4. map gene ids to protein ids
#  
#  ### get gene/protein ids via Biomart
#  mart=useMart(host = 'grch37.ensembl.org',
#               biomart='ENSEMBL_MART_ENSEMBL',
#               dataset='hsapiens_gene_ensembl')
#  
#  ### extract protein ids from the human network
#  protein_ids <- sapply(strsplit(rownames(adj_matrix), '\\.'),
#                        function(x) x[2])
#  
#  ### get protein to gene id mappings
#  mart_results <- getBM(attributes = c("ensembl_gene_id",
#                                       "ensembl_peptide_id"),
#                        filters = "ensembl_peptide_id", values = protein_ids,
#                        mart = mart)
#  
#  ### replace protein ids with gene ids
#  ix <- match(protein_ids, mart_results$ensembl_peptide_id)
#  ix <- ix[!is.na(ix)]
#  
#  newnames <- protein_ids
#  newnames[match(mart_results[ix,'ensembl_peptide_id'], newnames)] <-
#      mart_results[ix, 'ensembl_gene_id']
#  rownames(adj_matrix) <- newnames
#  colnames(adj_matrix) <- newnames
#  
#  ppi <- adj_matrix[!duplicated(newnames), !duplicated(newnames)]
#  nullrows <- Matrix::rowSums(ppi)==0
#  ppi <- ppi[!nullrows,!nullrows] ## ppi is the network with gene ids

## -----------------------------------------------------------------------------
sessionInfo()