similar to: [R-1.4.0] minimum spanning tree of large ontology

I KNOW this should be easy, but I'm stuck. My data frame consists of multiple observations from each of a number of stations, and what I would like to do is create another data frame that contains all the variables of the first, but only rows where a certain variable is at its maximum for the station. So, for example: > my.df stn obs v 1 1 1 0.26400396 2 2 1

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. >

Hello! I don't know if there is some R-package able to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance!

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

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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]]

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

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN

Full_Name: emiel ver loren Version: 2.2.0 OS: Windows XP Submission from: (NULL) (145.117.31.248) Dear R-community and developers, I have been trying to read in a tab delimeted file where the column names and the row names are of the form "GO:0000051" (gene ontology IDs). When using: > gomat<-read.table("test.txt") > colnames(gomat)[1] [1] "GO.0000051"

Dear cateGOry experts, hyperGTest documentation states that YEAST cannot be used as 'annotation' when evaluating gene ontology representation status for a given set of 'geneIds'. Because I am using a custom print I believe I need to create my own data package to use as the annotation file for 'annotation'. Can someone please describe how to make a data package that will

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

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

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On 11/14/08, David Flynn <davidf+nntp at woaf.net> wrote: > Correct; there is no metadata handling capability in the current > mapping spec. I'd suggest at some point to look into separate stream solution for metadata, perhaps M3F [1]. -Ivo [1] http://wiki.xiph.org/index.php/M3F

Hi, i want to parse a XML-File. I made some Tutorial but with my special Format it don't work. An Example of my format: <?xml version="1.0" encoding="ISO-8859-1"?> <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml

On Mon, Nov 17, 2008 at 11:41 AM, Ralph Giles <ralph.giles at artifex.com> wrote: > On Sun, Nov 16, 2008 at 3:22 PM, Silvia Pfeiffer > <silviapfeiffer1 at gmail.com> wrote: > >> Plus, the W3C is currently >> investigating a new ontology for video/audio metadata. This may be a >> good extension for vorbiscomment once finished. > > Ooh, can you say

Hello. R's e1071 package has "allShortestPaths" function using Floyd's algorithm. It is very useful for road network analysis. I'll try to analyze facility allocation programs using this. I'd like to know how much nodes this function can deal with? And for larger nodes(for example million nodes), allShortestPaths employs graph partition algorithm? Regards.

[ I''m still hoping for some help with this, folks... -r ] As part of the Arti (http://mephisto-ar.cfcl.com) effort, I''m looking into creating a database to store information on entities and relationships found in Ruby and Rails, as: Method M1 is defined for Class C1 in File F1. Method M1 of Class C1 is used by Method M2 in File F2. Disregarding (for the moment)

Dear R experts, I try to extract certain child nodes from an XML document and construct a table in which the parent node names are the columns and the child id values, joined in a list, are the cell content. If I first apply an XPath query to extract all above parent nodes, then iterate over those nodes and again apply a XPath query to select their child nodes, I get *ALL* matching child nodes

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library