Hello everyone, Im working with graphNEL object and want to extract all the nodes which have adjacent nodes with at least 20 nodes in between them. acc(graph, graphnodes) obviously provides a list for the accessable nodes of every node from a node and a number of the edges between them. Like this: $`hsa:8379` hsa:100131844 hsa:10393 hsa:246184 hsa:29882 hsa:29945 1 1 1 1 1 hsa:51433 hsa:51434 hsa:51529 hsa:64682 hsa:8697 1 1 1 1 1 $`hsa:51343` hsa:23594 hsa:23595 hsa:5001 hsa:5000 hsa:4999 hsa:4998 8 8 8 8 8 8 and so on. However I want know access the numbers so that I can compare these edgenumbers and only retrieve the nodes with an accessable node with at least 20 edges as mentioned above. How can I achieve this? In addtion whats the data type of the result of acc(). Is it a list in a list? Thank you

On 11/02/2012 10:23 AM, schaefe9 at informatik.uni-bonn.de wrote: > Hello everyone, > > Im working with graphNEL object and want to extract all the nodes which > have adjacent nodes with at least 20 nodes in between them. > > acc(graph, graphnodes) obviously provides a list for the accessable > nodes of every node from a node and a number of the edges between them. > Like this: > > $`hsa:8379` > hsa:100131844 hsa:10393 hsa:246184 hsa:29882 hsa:29945 > 1 1 1 1 1 > hsa:51433 hsa:51434 hsa:51529 hsa:64682 hsa:8697 > 1 1 1 1 1 > > $`hsa:51343` > hsa:23594 hsa:23595 hsa:5001 hsa:5000 hsa:4999 hsa:4998 > 8 8 8 8 8 8 > > and so on. However I want know access the numbers so that I can compare these > edgenumbers and only retrieve the nodes with an accessable node with at least > 20 edges as mentioned above. How can I achieve this? In addtion whats the do you mean you want these nodes acclist = acc(graph, graphnodes) len = sapply(acclist, length) keep = names(len)[len > 20] or maybe acc20plus = lapply(acclist, function(elt) elt[elt > 20]) keep = names(acc20plus)[!sapply(acc20plus, length) > 0] ? To create a subgraph of these, then subGraph(keep, graph) > data > type of the result of acc(). Is it a list in a list? ask the result class(acc(graph, graphnodes)) str(acc(graph, graphnodes)) or the help page ?acc -- it's a named list of named integer vectors. Check out RShowDoc("R-intro") for more help. Martin > > Thank you > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793