similar to: how to call Perl from R

Displaying 20 results from an estimated 2000 matches similar to: "how to call Perl from R"

2009 Aug 02
2
how to avoid a script from hanging up
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.
2009 Jan 27
3
plot Ticks
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]]
2008 Nov 11
1
R: R: Hidden Markov Models
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
2010 May 25
2
website address for the pseuso-XLS files
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
2009 Jun 16
2
R and miRecords
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
2010 May 26
2
how to avoid a subset of a matrix to become a column vector
I am assigning subset of a matrix A [n,3] where n>1 to a temporary matrix TMP I do not know how many rows of A will be assigned to TMP because this is established by a run-time test. I expect TMP to be a matrix [m,3], m >=1 But when 1 row only is transferred from A to TMP then TMP becomes [3,1] rather than [1,3] How can I avoid this unwanted transpose operation ? THank you in advance,
2009 Jun 23
2
question about package biomaRt
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]]
2009 Oct 30
2
MatLab SimBiology
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!
2009 Jul 28
2
Looking for example of usage of function unz
I would greatly appreciate some example of correct usage of function unz. I have to download and uncompress the following web compressef file: ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip I tried the following command that does not work: Targets.rec <- readLines(zz <- unz("ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip"))
2009 Mar 29
4
binary AND operators in R
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
2010 Feb 23
2
how to pass external parameters to an R script
How, if possible, can I run an R script, from command line, passing external parameters just like I can run a C main program passing parameters: # Cprog p1 p2 p3 Cprog can access its arguments (p1,p2,p3) through the built-in structures "argv" and "argc". Since R is built on C language I would expect the same feature to be available with R scripts as well ... ? Please, notice
2010 Jan 21
2
Updating R on Linux
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
2010 Apr 17
4
how to remove one row at a time from a matrix keeping its nrow consistent
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 <-
2009 May 24
2
how to implement a circular buffer with R
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
2010 May 25
2
how can I read a non-standard XLS file
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
2009 Apr 22
1
Color coded 3D plot
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
2010 Mar 03
1
R help unavailable
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
2010 May 27
3
how to extract the 1st field from a vector of strings
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]
2009 Aug 23
2
upgraging R from 2.9.0 to 2.9.1
I am still running 2.9.0 and came across a package that was built with 2.9.1. I got a warning upon loading the package. I tried to launch a function from such a package. It seems to hang up. I can't believe it takes forever. I am resolved to upgrade my R version to the newest one. But on a Windows box I do not know how to unistall the current version in advance of installing the new one. On
2009 Jan 03
4
passing parameters to an R script
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