similar to: question about package biomaRt

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

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,

I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the

I have attached a file downloaded from database mirWalk. Apparently it is in XLS format (this is the extension of the downloaded file). However, I cannot open it with OpenOffife spreadsheet program and Excel itself cannot separate the columns as it does when a true XLS file is loaded. I tried to read the attached downloaded file through R function "read.xls" and got the following

I have the following files list: > list.files() [1] "Prostate-Cancer_cvs_Dir" [2] "Prostate_Cancer-miRNAs&Genes.Pathway.xml" [3] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir" [4] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir.zip" [5] "Prostate-miRNAs.OrganTargets.txt"

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c" [4] "hsa-let-7d MIMAT0000065 Homo sapiens

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

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 am submitting this problem to the R forum , rather than the Bioconductor forum, because its nature is closer to programming style than any Bioinformatic contents. I have implemented an R script to extracts many strings through querying 3 Bioinformatic databases in the same loop cycle. Ideally, the script should perform as many cycles as necessary to extract all available data of interest.

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]]

Unluckily I dela with miRNA files whose name may contain the character "*". Because of the special meaning of "*" I have to remove it. I found out how to make list.files() extract only those file names which contain a "*" Namely: # list.files(pattern="\\*") Now I have to process all files whose name does NOT contain the character "*". I cannot

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 <-

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 <-

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 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

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 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

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

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