[R] Directory operations

[Don MacQueen]

To initialize an list:

>  foo <- list()

## and then extend it as in your code
>  foo <- c(foo, list(x=1))
>  foo
$x
[1] 1

>  foo <- c(foo, list(y=1))
>  foo
$x
[1] 1

$y
[1] 1

At 7:16 PM +0530 1/10/10, anupam sinha wrote:
>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
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>>  ______________________________________________
>>>>>  R-help at r-project.org mailing list
>>>>>  https://*stat.ethz.ch/mailman/listinfo/r-help
>>>>>  PLEASE do read the posting guide
>>>>>  http://*www.*R-project.org/posting-guide.html<
>>>>>  http://*www.*r-project.org/posting-guide.html>
>>>>>
>>>>>  and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>>
>>>>
>>>>
>>>>  --
>>>>  Jim Holtman
>>>>  Cincinnati, OH
>>>>  +1 513 646 9390
>>>>
>>>>  What is the problem that you are trying to solve?
>>>>
>>>>
>>>
>>>
>>>
>
>
>--
>Graduate Student,
>Laboratory of Computtational Biology,
>Centre For DNA Fingerprinting And Diagnostics,
>4-1-714 to 725/2, Tuljaguda complex
>Mozamzahi Road, Nampally,
>Hyderabad-500001
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list
>https://*stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://*www.*R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.


-- 
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062