title: Creating Subgraph using igraph in R
body: <p>I need to obtain a subgraph of the seed nodes (the input list of nodes; file.txt) and their first interactors (neighbours) from a graph (g) using igraph. Unfortunately, I am ending up with only a single node in the subgraph, and not all the rest of the nodes and edges (vertices) which interlink them. </p>
  
  <pre><code>g&lt;-read.graph("DATABASE.ncol",format="ncol",directed=FALSE) #load the data
  g2&lt;-simplify(g, remove.multiple=TRUE, remove.loops=TRUE) # Remove the self-loops in the data
  DAT1 &lt;- readLines("file.txt")   #It provides a character vector right away
  list_nodes_1 = neighbors(g2, DAT1) #list of nodes to be fetched in subnetwork
  list_nodes_1 # 16
  g3 &lt;- induced.subgraph(graph=g2,vids=DAT1) #subnetwork construction
  g3 # GRAPH UN-- 1 0 --; indicating only one node
  plot (g3)
  </code></pre>
  
  <p>Any suggestions for obtaining the whole subnetwork (including nodes and vertices)? or is there any other function available for creating sub-graphs?</p>
  
  <p><strong>DATABASE.ncol:</strong> </p>
  
  <pre><code>MAP2K4  FLNC
  MYPN    ACTN2
  ACVR1   FNTA
  GATA2   PML
  RPA2    STAT3
  ARF1    GGA3
  ARF3    ARFIP2
  ARF3    ARFIP1
  XRN1    ALDOA
  APP     APPBP2
  APLP1   DAB1
  CITED2  TFAP2A
  EP300   TFAP2A
  APOB    MTTP
  ARRB2   RALGDS
  CSF1R   GRB2
  PRRC2A  GRB2
  LSM1    NARS
  SLC4A1  SLC4A1AP
  BCL3    BARD1
  </code></pre>
  
  <p>It is a simple text file with one edge per line. An edge is defined by two symbolic vertex names delimited by tab:</p>
  
  <p><strong>file.txt</strong></p>
  
  <pre><code>ALDOA
  APLP1
  GRB2
  RPA2
  FLNC
  BCL3
  APP
  RALGDS
  PRRC2A
  NARS
  LSM1
  GGA3
  FNTA
  </code></pre>