similar to: connectivity measure for graph nodes

I'm doing some work on a potential patch to the Bioconductor package Rgraphviz and have some questions on code that is contained in engine.c. In particular, I am developing some custom shapes using polygon and need to make sure that, with rendering, the line connecting the centers of two polygons stops at the border of each polygon. The polygons can be transparent, so the option of just

I am getting some unexpected results from some functions of igraph and it is possible that I am misinterpreting the vertex numbers. Eg., the max betweenness measure seems to be from a vertex that is not connected to a single other vertex. Below if my code snippet: require(igraph) my.graph <- graph.adjacency(adjmatrix = my.adj.matrix, mode=c("undirected")) most.between.vert <-

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive graph displays but R crashes. See my sessionInfo() and a short example below. Ggobi and rggobi installed without complaints. Mark > sessionInfo() R version 2.7.0 Patched (2008-05-04 r45620) x86_64-unknown-linux-gnu locale:

I have a very long list that I'd like to subset based on a logical value within each element. Example below. I'd like to get just those list elements for further study whose $sig.cor slot is TRUE. In this example, I'd only want element [[2]]. Should be simple, I know. How can I do this? Thanks, Mark > gene.pair.tf.lst [[1]] [[1]]$gene.pair [1] "Lgals1:Pxmp2"

I was running some sample code from a help page tonight and wished to redirect the sample output to my Desktop under Linux (Mint-Debian 64 if it makes a different). I was surprised to find that file name expansion using the ubuquitious "~/" was not recognized, in fact it caused R to crash. Is this expected behavior? See my output below and sessionInfo(). Also, not shown, but

I have identical R.profiles and R_HOME directories set up on both my local machine and a remote linux cluster. To keep my libraries and R install separate, I use a site-library on both machines. The first line of my .Rprofile is: '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' Until R-2.6.0 this was working fine on both machines, but since I have been

I have a list (length 750), each element containing a vector of unique strings (unique gene ids), with length up to ~40 (median 15). I want to compile a matrix of all possible triplets and their frequency within gene elements. Using combn and a lot of looping, I am accomplishing this but it is VERY slow. I've tried to figure out a way to vectorize this, using "match" and

I have used merge regularly and thought I understood how it worked, but I must not. I have two dataframes with identical colnames from two different experiments, TL01 and LC01. Each dataframe has a column named "Entrez.Gene", which I have converted to "as.character" just to make sure merge is not looking at factor levels. Because I have done some filtering, the Entrez.Gene

After some struggling with the data format, non-standard in BioConductor, I have gotten cor.balance in package CORREP to work. My desire was to obtain maximum-likelihood p-values from the same data object using cor.LRtest, but it appears that this function wants something different, which I can't figure out from the documentation. Briefly, my dataset consists of 36 samples from 12

I am using grep to locate colnames to automate a report build and have run into a problem when a colname is not found. The use of integer(0) in a conditional statement seems to be a no no as it has length 0. Below is a self-contained trivial example. I would like to get something like "NA" or -1 for the position when it is not found OR learn a way to use integer(0) or some

I'm having trouble with a Bioconductor package, an variable expected in an environment does not seem to be there. As part of my investigation of the problem (most likely on my end) I'd like to list the variables contained in an environment. If you have an environment loaded, lets call it "pkgEnv', how does one find what it does contain? Mark

Is it possible to vectorize anova over the output of a vectorized lm? I have a gene expression matrix with each row being a gene and columns for samples. There are several factors with interactions. I can get p values by looping over the matrix with lm and anova, but I would like to make this as computationally efficient as possible. I am able to vectorize the lm command, but when I try to use

I need to write a table that can be opened in Excel or OpenOffice such that there are newlines embedded within cells. After much Googling and futzing, I can't figure out how to do this. The way to do this within Excel is alt-Enter and I've tried '/n', '/n/r', '/r/n' per some web suggestions without luck. Anybody know what character or ASCII code to use for this?

Switched back to R-devel tonight after using R-2.6.1 for awhile and when I updated my devel packages Matrix installation failed. Not critical for me but thought I should report it. I am using Ubuntu Gusty AMD64 OS. Tail of install output and sessionInfo follows. Mark Loading required package: methods Loading required package: lattice Attaching package: 'Matrix' The

I'm having trouble achieving the results I want using a regular expression. I want to eliminate all characters that fall within square brackets as well as the brackets themselves, returning an "". I'm not sure if it's R's use of double slash escapes or something else that is tripping me up. If I only use one slash I get 1: '\[' is an unrecognized escape in a

I am performing many permutations on a data-set with each permutation producing a variable number of results. I thought that the best way to keep track of all this in one object would be with a list ('res.lst'). To address these variable results for each permutation I attempted to construct this list using 'assign'. There is even more nesting than indicated below, but this is a

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

I'm using the command below on an open3d() object to create a shaded cube. Changes to myScalingFactor do not effect changes in the size of the cube. What is the correct approach? Mark shade3d(translate3d(cube3d(identityMatrix() * myScalingFactor),-6,1,-1),col="green", alpha = 0.2) -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine

I am familiar with packages that read and write Excel files on both Windows and Linux platforms. Do any packages provide similar functionality for MS Word files? I have a lot of text processing to do and the text is embedded in ~200 different Word files (.doc format Office 2003). All I need to do is read, not write. Thanks, Mark ------------------------------------------------------------ Mark