Directory operations

 foo <- list()

 foo <- c(foo, list(x=1))
 foo

 foo <- c(foo, list(y=1))
 foo

Hi Uwe,
             Thanks for your suggestion . Here's my code. I am confused as
to how to initialize an empty list . Here I have used pairlist()


 *list.files()->org_xml_dirs
 for (i in org_xml_dirs)
{
 setwd(file.path("/home/anupam/Research/Anupam_data/ORG_XML_FILES/",i))
 org_xml<-list.files()
 for(j in org_xml)
 {
 graph_list<-pairlist()
 graph<-parseKGML2Graph(j,genesOnly=TRUE)
 graph_list<-c(graph_list,list(graph))
 }
 org_met_net<-mergeKEGGgraphs(graph_list)
 met_org<-igraph.from.graphNEL(org_met_net,name=TRUE)

write.graph(met_org,"/home/anupam/Research/Anupam_data/ORG_XML_FILES/i.metnet",format=c("NCOL"))
 }
*
This is giving an error:

Error in UseMethod("xmlAttrs", node) :
  no applicable method for "xmlAttrs"

I apologise for asking a Bioconductor list related question on this list.
Can you figure out the problem ? Thanks in advance.


Regards,

Anupam


On Sun, Jan 10, 2010 at 12:54 AM, Uwe Ligges <
ligges at statistik.tu-dortmund.de> wrote:

 On 09.01.2010 19:04, anupam sinha wrote:

 Hi Jim,
             Thanks for your suggestion. I tried scripting but gives me an
 error. Can you tell me what am I doing wrong here ?


 *>  list.files()->org_xml_dirs

 Please do turn that arrow around....


  for (i in org_xml_dirs){

 + setwd("/home/anupam/Research/Anupam_data/ORG_XML_FILES/i")}

 There is no directory .../i
 Your probably want:
 setwd(file.path("/home/anupam/Research/Anupam_data/ORG_XML_FILES/", i))

 Uwe Ligges
 >
 >
 >
 >

 >>   Error in setwd("/home/anupam/Research/Anupam_data/ORG_XML_FILES/i") :
 >>   cannot change working directory
 >> *
 >>
 >>
 >> On Fri, Jan 8, 2010 at 11:37 PM, jim holtman<jholtman at gmail.com>  wrote:

  ?list.files

 ?file.info
 ?setwd

 You can get a list of all the files in a directory (list.files) and then
 do
 a file.info to determine which ones are the directories you want to
 search.  A list.files on that directory will give you the list of file
 names
 that you can then process.




 On Fri, Jan 8, 2010 at 12:41 PM, anupam sinha<anupam.contact at gmail.com

 >wrote:

  Dear all,

              I have this directory structure :

 Dir1       Dir2       Dir3      Dir4  .........................
 A.xml     D.xml    G.xml
 B.xml     E.xml     H.xml
 C.xml     F.xml     I.xml

 Within each of these directories (Dir1, Dir2 etc) there are a num of xml
 files (A.xml, B.xml etc).

 What I want to do is to enter into the first directory read all the xml
 files do certain operations come out  of the directory and do the same
 thing
 for another directory. Can anyone help me out ? Thanks in advance for
 any
 suggestions.

 Regards,

 Anupam Sinha

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 Jim Holtman
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