Displaying 20 results from an estimated 500 matches similar to: "gene ontology association"
2002 Nov 04
3
write table and dinnames
I would write in tab-text file a table like this one:
TAB colname1 TAB colname2 TAB TAB... colnameN
rowname1 # # #
rowname2 # # #
rownameM # # #
then I wrote something like:
mymatrix <- matrix(nrow=M,ncol=N,byrow=T)
rownames(mymatrix) <- chvector1
colnames(mymatrix) <- chvector2
2008 May 05
1
computational ontology to research questions, and statistical methods
our group at Duke is currently attempting to connect two data sets fed
through a web-based system, one containing research questions (i.e.,
variables positioned with certain roles) and a database of statistical
methods. this connection is done informally in a number of R packages
and related software such as Rcmdr, R4calc, and Rkward where a
variable of a certain type is matched to a certain
2003 Jan 22
1
self-split plot on multiple device
Hello!
I would plot more than 10 (this number is always different)
graphics on a figure with layout like 'mfrow=c(4,2)'.
There is some existing function able to open the right number of
device if number of graphics is done or I have to build it myself
with some 'IF.....ELSE.....'?
Thanks.
A.S.
----------------------------
2010 Oct 11
1
Response to your LC Comment -2393 on Media Ontology spec
Dear Jean-Marc:
Would you please send Thierry an ontology mapping table specification
for speex according to the format he links to at the end of his
message below? Thank you.
On Mon, Oct 11, 2010 at 9:54 AM, Thierry MICHEL <tmichel at w3.org> wrote:
> Dear James,
>
> In your latest email to the MAWG response to your comment, you seem to
> disagree with the MAWG proposal.
>
2011 May 18
2
Query Gene ontology
Un texte encapsul? et encod? dans un jeu de caract?res inconnu a ?t? nettoy?...
Nom : non disponible
URL : <https://stat.ethz.ch/pipermail/r-help/attachments/20110518/a7d31ce9/attachment.pl>
2002 Jan 21
1
[R-1.4.0] minimum spanning tree of large ontology
Dear all,
I have an ontology which I would like to load in R to then compute the
minimum distance between elements.
Since this ontology is not only DAG, the problem is non trivial and
therefore decided to use R with the powerful e1071
library (allShortestPaths) to do that. That method requires to provide a
distance matrix between the
various objects. My ontology contains 32768 objects and
2002 Oct 28
3
create an object list in a loop
Hi! Probably I perform this question because I did'nt still understand the
R-philosophy.
I have to build many matrix, with different dimensions, and I would to
assign them a
same 'prefix' name, i.e. "aval", but, obviuosly different suffix, something
like:
for (i in 1:n) {
aval%i% <- matrix(scan(data....),nrow=nr[i],ncol=nc[i]
...
}
where "%i%"
2002 Nov 06
2
chisq.test on a matrix
Hello!
What kind of calculation perform 'chisq.test', if its argument is a matrix?
Thanks for any suggestion!
------------------------------------------------------------
Sincerely yours.
Dr. Alessandro Semeria Tel. +39 544 536811
Models and Simulation Lab of Fax. +39 544
538663
The Environment Research Center - Montecatini
2010 Jun 16
1
Is there any function to read genbank flat files.
Hi
I am trying to read genbank est flat files. Is there any function in R to do
that. I was looking for something similar to SeqIO.parse(input_handle,
"genbank") in bioPython that convert the genebank sequence into fasta
sequence.
(One option is to call biopython from R but I am not familiar with python
functions so I want to avoid that and I am keeping it as last resort)
Thanks and
2012 Apr 03
2
how to map microarray probe to gene, homology
Hi:
I have clustered microarray gene expression data and trying to map between
microarray probe, gene, pathway, gene ontology, and homology for a set of
(affy) microarray probes. Is there any package in R which facilitates this?
I am looking at bioconductor, but till now could not find a solution. A
link to some worked example would be appreciated.
Thanks and regards.
John
[[alternative HTML
2010 Jun 10
1
OWL ontologies in R?
Are there any R packages to import and use Web Ontology Language (OWL)
ontologies (represented in OWL/RDF or other form)?
Thanks,
-s
[[alternative HTML version deleted]]
2004 Sep 25
2
Strange behavior of is.na() on lists
Hello R-users,
I have observed that is.na() behaves strange on some lists. Here is a
simple example:
> a = list(list('asd'))
> a
[[1]]
[[1]][[1]]
[1] "asd"
> for(i in 1:5)
+ print(is.na(a))
[1] TRUE
[1] FALSE
[1] TRUE
[1] TRUE
[1] TRUE
>
> for(i in 1:10)
+ print(as.integer(is.na(a)))
[1] 0
[1] 10
[1] 1
[1] 0
[1] 140897024
[1] 134567568
[1] 1
[1] 1953720684
2007 Aug 16
1
use AnnBuilderSourceUrls with local path insted of ftp adress
Hallo everybody.
I want to build my own GO package using the function GOPkgBuilder of AnnBuilder. It uses AnnBuilderSourceUrls to collect data from different ftp sites. These data are not complete for my organism, so I would like to change the ftp adresses to a local one. The changing itself is working but when I run the script I get the following Error:
Error in
2008 Oct 17
2
R script from Python
Hi,
I'm trying to execute R-script from Python. I'm using R 2.7.2, Python 2.5
and WinXP.
I don't won't to use Python/R interface because of nature of project.
Python code :
import subprocess
command = 'c:\\Program Files\\R\\R-2.7.2\\bin\\Rterm.exe --vanilla -q
<d:\\test\\run\\geneBank.r> d:\\output.out'
subprocess.Popen(command).wait()
After that, I get error
2007 Aug 19
1
Building Packages with AnnBuilder
Hi there.
I got some Problems building an Annotation-Package with AnnBuilder.
Not using the function ABPkgBuilder(), but just parts of it to create a
package without connecting to the servers, I managed to create a Package,
but it seems to be empty. R recognizes it as a package, but is unable to
load it.
The form of the data is in a correct form, I got an example-annotation-file
the function
2003 Apr 28
4
plot(pam.object) error with R-1.7.0 on Red-Hat 8.0 i686
I don't know if there is some fault in compiling or a bug of the new
R-1.7.0 version:
cl.pam.2 <- pam(as.dist(1-cor(mel.data)),2)
plot(cl.pam.2)
perform a right partitioning and silhouette plot on the old R-1.6.2
instead
"Error in clusplot.default(x$diss,...... ;
x is not numeric"
is the output on the new R-1.7.0.
Same platform: RH8.0 i686.
Some suggestions?
A.S.
2004 Nov 11
5
expressions and paste
I have written a function to plot data which will be used for various different chemistries.
A simplified version is:
plot_data <- function(risk,levels,chem,sd2,measure){
plot(risk, levels,main=paste ("per", sd2, measure, "\n in usual", chem))
}
The problem is with the title.
This works fine if the variable "chem" is just text, but if it is an expression then
2003 May 29
0
Bioconductor 1.2 Released
The Bioconductor development team announces release 1.2 of the
Bioconductor packages for the analysis of genomic data. Bioconductor
is an open source bioinformatics software project based on the R language.
Version 1.2 features:
=====================
* All packages from the 1.1 release are included. All current bug
fixes have been applied, and most have been upgraded and
provide enhanced
2004 Apr 02
1
which on array
Good morning !
Today I found a strange, for my poor knowledge of R, behaviour of
'which' on a matrix:
HAL9000> str(cluster.matrix)
num [1:227, 1:6300] 2 2 2 2 2 2 2 2 2 2 ...
HAL9000> class(cluster.matrix)
[1] "matrix"
HAL9000> ase <- cluster.matrix[1:5,1:5]
HAL9000> ase
[,1] [,2] [,3] [,4] [,5]
[1,] 2 2 2 0 -2
[2,] 2 2 2 0 -2
[3,]
2003 Oct 23
7
generic algorithm
Dear all,
Is there any generic algorithm code for optimization implemented in R? I
searched without success.
Thanks,
--
Zhu Wang
Statistical Science Department
Southern Methodist University
Phone: (214)768-2453
Fax: (214)768-4035
Email: zhuw at mail.smu.edu