similar to: help with installation of local gzip-ped packages

I wonder whether R provides an interface to access miRecords data. Particularly, I am looking for extracting humans miRNA and target genes sequences. All such information is stored in there in a set of structured web site pages (http://mirecords.umn.edu/miRecords) I would greatly appreciate any suggestion even about other data bases from where it is possible to get the same sort of data. I had a

Is there a way to force the number of ticks along an axis ? I read the on-line documentation and tried many combinations of all available parameters from functions par(), axTicks(), axis(), plot() ... but no luck ! Thank you very much, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

I have the following vector of strings (shown only the first 3 elements) > desc[1:3] [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7a* MIMAT0004481 Homo sapiens let-7a*" [3] "hsa-let-7a-2* MIMAT0010195 Homo sapiens let-7a-2*" > is.vector(desc) [1] TRUE > A <- unlist(strsplit(desc[1:3], " ")) > A [1]

After some headache with debugging my script, I finally isolated the problem taht I am going to illustrate in the following example. I expected matrix nrow to decrease consistently till 1. Instead, when the matrix is left with one row only, its nrow jumps to 2 because the matrix gets transposed. How come ? Thank you, Maura > B <- c(1,2) > B <- rbind(B,c(3,4)) > B <-

Can biomaRt connect to data base "http://mirecords.umn.edu" or a branch of it ... for instance the validated miRNAs list ..? Thank you very much. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Is there any R package that implements the same capability of MatLab toolbox called SimBiology ? We are expecially interested in protein-protein interactions and network analysis. As far as I know SimBiology implements a system of ODEs reflecting the kinetic chemical reactions. We would be more interested in stochastic simulations. Thank you in advance. Maura tutti i telefonini TIM!

I tried to use R version of package I noticed the original MatLab Pckage is much better documented. I had a look at the R demo code "gtm_demo" and found that variable Y is used in advanced of being created: I wrote my own few lines as follows: inDir <- "C:/Documents and Settings/Monville/Alanine Dipeptide/DBP1/DHA" setwd(inDir) T <-

http://gigamail.rossoalice.alice.it/messages/readMessageFrameset.aspx?DeliveryID=ba40cf18-29db-4404-a3ce-af26f760ecf9 Please, paste the website address above shown in your web browser address field. Make sure the whole string is pasted with no space or any other character. Telecom couldn't generate more clumsy website addresses .... Sorry for that. Thank you in advance, Maura tutti i

Thank you for your prompt answer. The breathing signal observations are the amplitude values as a function of time and phase. According to our model the hidden states are the different breathing types. Subjects, whose respiratiion process is regular, are likely to breathe, keeping the same cycle pattern/type, for many consecutive cycles. therefore dwelling in the same hidden state. The more

I cannot find any R function or operator that performs a binary AND operation, as performed by Fortran built-in function "iand". Ideally either R operator "&" or "&&" should do that. But some tests proved they do not: > A<- 1 > B <- 2 > A [1] 1 > B [1] 2 > as.numeric(A&B) [1] 1 > as.numeric(A&&B) [1] 1 The binary

I knowf R functions ca be called passing some parameters. My first question is: how are parameters passed to R functions ? Browsing through R archives I found an answer confirming taht parameters can be passed to the called function by value. I wonder whether passing the parameter address is possible somehow to allow the function to actually change its value. My second question is about

I am running the last R version on SuSE 11.1. I installed the Bioconductor environment following the instructions on the web. As a consequence some core packages from Bioconductors were installed. I need to add some more packages. So I tried biomaRt as follows. It does not get installed correctly. Please see the following sequence. Thank you in advance. Maura >

I know my question has been asked many times. Please, forgive me for asking it once more. It's time to update R version. I run R on Windows, Linux, and Mac OS/X. I think I remember on Windows R comes with the un-installer. So I uninstall it first and then I install the latest version. On Mac OS I have no experience of updating R ... I think (and hope) all what I have to do is to drag R icon

Some wavelet analysis experts have implemented periodic boundary conditions for signals. I need to implement a circular buffer. Something like: "12345abcdefgh12345abcdefgh" so that at each step the riightmost element is moved to the leftmost index and everything else is properly shifted: "h12345abcdefgh12345abcdefg", "gh12345abcdefgh12345abcdef", .... My

I wonder whether it is possible in R to generate color-coded 3D plots, like the attached example. Basically a function f(x,y) (the 3rd dimension) is rendered through colors intensities. The side color-bar is a guide to the interpretation of the plot. Thank you very much, Maura e tutti i telefonini TIM! Vai su e tutti i telefonini TIM! Vai su

I have recently replaced R-2.9.0 with R-2.10.1 Patched. Apparently the installation completed successfully but right now I realized that the on-line help does not work any more. When I type "?<R-command>" a message pops up warning that "Help will not be available. Path not found" ... regardless of the R-command. How can I get back R on-line man pages ? Thank you very

I deal with a huge amount of Biology data stored in different databases. The databases belongig to Bioconductor organization can be accessed through Bioconductor packages. Unluckily some useful data is stored in databases like, for instance, miRDB, miRecords, etc ... which offer just an interactive HTML interface. See for instance http://mirdb.org/cgi-bin/search.cgi,

here is the message I get upon trying to upgrade R from the provided RPM package for SuSE 11.1 (http://cran.r-project.org): #### YaST2 conflicts list - generated 2010-02-15 14:00:50 #### nothing provides libreadline.so.6()(64bit) needed by R-patched-2.10.1-50.1.x86_64 [ ] do not install R-patched-2.10.1-50.1.x86_64 #### YaST2 conflicts list END ### I searched for the requested library

I am going to try out a tentative clustering of some feature vectors. The range of values spanned by the three items making up the features vector is quite different: Item-1 goes roughly from 70 to 525 (integer numbers only) Item-2 is in-between 0 and 1 (all real numbers between 0 and 1) Item-3 goes from 1 to 10 (integer numbers only) In order to spread out Item-2 even further I might try to

After a year my R programming style is still very "C like". I am still writing a lot of "for loops" and finding it difficult to recognize where, in place of loops, I could just do the same with one line of code, using "sapply", "lapply", or the like. On-line examples for such high level function do not help me. Even if, sooner or later, I am getting my R