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 <
lig...@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<jholt...@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.cont...@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@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
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Hyderabad-500001
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