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 <
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
Mozamzahi Road, Nampally,
Hyderabad-500001
[[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
and provide commented, minimal, self-contained, reproducible code.
--
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062
______________________________________________
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
and provide commented, minimal, self-contained, reproducible code.
