similar to: Can't use attributes from gml file in Cytoscape

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 Everyone! This is my first post to the mailing list so please forgive me if I am a bit deflected from the general format of this mailing list posts. Since I need help in this matter urgently, I would cover up any of my mistakes in posting later. That said, I have a problem in merging 2 graphs that have common nodes between them. I have a graph G1, that have nodes N1 and edge set E1 and

Hi, is there anyone here who succeed to run any 3D software at good speed with such 3D hardware ? On my side, 3D accelleration is ok with Xorg and pure linux game (xmoto for example run really fine). Is there anything to do with Wine to allow programs runs under it to work as "native" Linux software ? Have I miss something somewhere ? (I think of wine compilation and especially

Hello, I'm having a look at section 13.1 from SIP Connect v2 doc (see [1]). It refers to RFC6442 which gives the following example (sorry for its length): INVITE sips:bob at biloxi.example.com SIP/2.0 Via: SIPS/2.0/TLS pc33.atlanta.example.com;branch=z9hG4bK74bf9 Max-Forwards: 70 To: Bob <sips:bob at biloxi.example.com> From: Alice <sips:alice at

I realize that matrix indexing has been addressed in various flavors, but I''m stumped and didn''t find anything in the archives. It''s not clear if it is an igraph issue or a more general problem. Thanks in advance for your patience. I am using igraph to read a gml file (http://www-personal.umich.edu/~mejn/netdata/football.zip ). The gml file contains vertex attributes

Dear Catarina, I prefer to leave the AIC value as NA for the tweedie GLM family because it takes extra time to compute and is only occasionally wanted. It's easy to compute the AIC yourself using the dtweedie() function of the tweedie package. Best wishes Gordon At 03:05 AM 14/08/2007, Catarina Miranda wrote: >Dear Gordon; > >I have also sent this email to R help mailing list,

Hi, I'm trying to use the XML-RPC client in the SSOAP package to connect to a service that I have created. From other languages (Perl, Python, Ruby) this is not a problem but the SSOAP client gives the following error: Error in .XMLRPC("http://localhost:9000", "Cytoscape.test", .opts = list(verbose = TRUE)) : Failed to parse XML-RPC request: Content is not allowed in

Hi there, How may I smooth spline two vectors with the smoothing parameter selected by generalized maximum likelihood (GML) .? Thanks a lot. -- View this message in context: http://r.789695.n4.nabble.com/Smoothing-spline-with-smoothing-parameters-selected-by-generalized-maximum-likelihood-tp4210679p4210679.html Sent from the R help mailing list archive at Nabble.com.

I have compiled R version 1.3.1 on a Linux system. No errors or warnings are reported. However, "make check" fails thus: ===== make[5]: Leaving directory `/proj/informatics-build/GML/R/R-1.3.1/src/library' running code in base-Ex.R ... ../../bin/R --vanilla < base-Ex.R > base-Ex.Rout make[4]: *** [base-Ex.Rout] Error 139 ===== The base-Ex.Rout being produced at this

Dear R-list. I'm doing af logistic analyses using gml. The model explaines variations in Adverse events infections (0 og 1) using age as explanatory variable. model2d<-glm(formula=AEorSAEInfecBac~Age,family=binomial("logit"),data=emrisk) I want to get predictions with 95% confidence limits for age 30 and age 60. I've been reading the "google" and "search

Hi Can some one please point out where i am wrong. I am trying to position set of nodes column-wise in cytoscape using RCytoscape A----D B----E C----F ------------------- g <- new ('graphNEL', edgemode='undirected') cw <- CytoscapeWindow ('smallExample', graph=RCytoscape::makeSimpleGraph()) layout (cw, 'jgraph-spring') redraw(cw) nodesFr = c('A',

I have a large correlation matrix that I'm trying to convert to a list of every connection (edge) between every two nodes with its accompanying correlation value (for Cytoscape). I figured out how to do this and to remove the connections that nodes have to themselves but I can't figure out how to get rid of the duplicate pairs (e.g. the edge b-a is a duplicate of a-b).

On Mon, Oct 9, 2017 at 4:42 PM, Tom Callaway <tcallawa at redhat.com> wrote: > > On 10/09/2017 11:16 AM, Paul Smith wrote: >> >> I am trying to install >> >> igraph package >> >> but getting the following error: >> >> ------------------ >> make: *** [/usr/lib64/R/etc/Makeconf:159: foreign-graphml.o] Error 1 >> ERROR:

Hello: I've been trying for days now to get igraph working on a debian sarge install. There does not appear to be any pre-built packages, and when I try and install within R, it blows up on the final linking, claiming its unable to find libgfortran (which IS installed, and IS working for all other users of the compiler). I started up R and ran: install.packages("igraph"). It

Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best, Tim [[alternative HTML version deleted]]

After writing some code (stupidly without checking to see if there was code to do this already) to generate PostGIS SQL insert statements for simple geometry (wkt), I didn't check see if there is already something available to convert WKT strings into some R package geometry (sp?). Does anyone have any advice, hints, code (?) for converting the following OpenGIS strings into something

Dear R users, I would like to draw map and import it in maptools/spatstat packages. The 'raw data' I have come from a web page (<map>...</map>) and are basically a list of coordinates of a polygon. I would like to know how to import them in R; I checked the maptools packages, but all the examples use existing .dbf files. I just have a (serie of) text file(s) looking like

Hi all, I was quite succesfully working with the RODB package on a 32 bit linux box to connect to a MSSQL Server via the freeTSL driver. After changing to a 64 bit environment I ran into some segmentation faults using function sqlUpdate on large database operations (the actual seg faults occured in the call to the C function ODBCUpdate). I just briefly looked into the code and found some extensive

Dear All, I am trying to install igraph package but getting the following error: ------------------ make: *** [/usr/lib64/R/etc/Makeconf:159: foreign-graphml.o] Error 1 ERROR: compilation failed for package ?igraph? * removing ?/usr/lib64/R/library/igraph? ------------------ Any ideas? Thanks in advance, Paul

Hello, I want to call glm inside a function. In the first lines of code I build the weights, the formula, ... and then I call glm with the following command: glm(formularesp, data=data, family=familyresp, weights=eval(data$weights) My problem is that the fitting proccess is performed just like if weights=NULL, even if my weights are not equals to 1. I've performed some return() command