[R] [R-pkgs] Version 1.0 of hapassoc now available from CRAN
Version 1.0 of hapassoc now available from CRAN hapassoc is an R package for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm. Recent changes include the addition of anova and logLik methods for the class hapassoc, to allow users to perform likelihood ratio tests of haplotype effects. Other changes include bug-fixes and improvements to the documentation, such as the addition of a package vignette. See the exerpt from the ChangeLog for more details. ChangeLog 2006-04-04 Version 1.0 * hapassoc(): the baseline argument is documented to have default equal to the most common haplotype, but the code to implement this default was lost and needed to be replaced. * hapassoc(): added a verbose flag. Default is verbose=FALSE. If TRUE users see the iteration number and value of the convergence criterion at each iteration of the EM algorithm. * pre.hapassoc(): added a verbose flag. Default is verbose=TRUE. If TRUE users see a list of the SNP genotypes used to form haplotypes and a list of the other non-haplotype variables. * Package vignette hapassoc added. After loading the package, type vignette(hapassoc) to view. 2006-03-22 * Overall addition of the log-likelihood functions * hapassoc(): function now returns log-likelihood and model * logLik.hapassoc(): New function to extract the log-likelihood from a hapassoc object * anova.hapassoc(): New function to perform likelihood ratio test on two hapassoc objects. 2006-02-02 Minor changes: * EMvar(): fixed a bug occurring when all haplotype phases are known. * RecodeHaplos(): fixed a bug where a single column of non-haplotype data in a non-allelic data set was losing its name. * hapassoc(): Change ... argument of hapassoc to start. Previously the only intended use of ... was to allow the user to pass in start for starting values to the glm function, rather than to allow the user to pass in other optional arguments to glm. We have now made this more explicit by making this argument more specific. ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] handling warning messages
Is there any way to store the value of warnings but avoid printing them? A simplified example: out - c(0.2,0.3,0.4) var - c(2,3,4) outcome - glm(out ~ var, family=binomial()) Warning message: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) I don't like the warning printed, but I would like to be able to check it's value after the top-level function has completed and than decide weather to print it or not. Thanks, Sigal Blay Statistical Genetics Working Group Department of Statistics and Actuarial Science Simon Fraser University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [R-pkgs] New version of the LDheatmap package
Version 0.2 of the package LDheatmap is now on CRAN. The main function LDheatmap produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The revisions to the package are aimed at improving the user's ability to modify and annotate the heatmap. Most notably, LDheatmap is now based on grid graphics. Examples of how to modify the plot using tools from the grid package are included in the LDheatmap help file. Sigal Blay ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ERROR: installing package indices failed
Turns out that this problem is a propagation of a bug from a Depends package - gdata doesn't import stats in its NAMESPACE file, although it makes use of objects defined in stats like reorder and na.omit. I'm curious as to the reason why 'R CMD check' did not detect this at the source package, and instead did not pass my new package. Something for you mighty R developers to consider? Thanks, Sigal Blay On Sun, Nov 21, 2004 at 05:19:46PM +0100, Uwe Ligges wrote: Sigal Blay wrote: gregmisc is installed yet the problem persist. I installed gregmisc using install.packages(c(combinat,gregmisc,genetics),lib='/home/sblay/lib') (on the same library path where I am trying to install LDheatmap) Have you set the environment variable R_LIBS appropriately? Uwe Ligges installed.packages(lib='/home/sblay/lib') Package LibPath Version Priority Bundle combinat combinat /home/sblay/lib 0.0-5 NA NA gdata gdata /home/sblay/lib 2.0.0 NA gregmisc genetics genetics /home/sblay/lib 1.1.1 NA NA gmodels gmodels /home/sblay/lib 2.0.0 NA gregmisc gplotsgplots/home/sblay/lib 2.0.0 NA gregmisc gtoolsgtools/home/sblay/lib 2.0.0 NA gregmisc LDheatmap LDheatmap /home/sblay/lib 1.0 NA NA ... I am developing a package named LDehatmap. It depends on the genetics package and includes two data files and a demo file. When I'm trying to install it, I get the following messages: * Installing *source* package 'LDheatmap' ... ** R ** data ** demo ** help Building/Updating help pages for package 'LDheatmap' Formats: text html latex example LDheatmaptexthtmllatex example ldheatmaptexthtmllatex example Error: object 'reorder' not found whilst loading namespace 'gdata' Error: package 'gdata' could not be loaded Execution halted ERROR: installing package indices failed Any ideas? Yes. You do not have gdata (part of gregmisc) installed, and genetics depends on it. How did you get genetics installed? A binary install? Install gregmisc __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ERROR: installing package indices failed
gregmisc is installed yet the problem persist. I installed gregmisc using install.packages(c(combinat,gregmisc,genetics),lib='/home/sblay/lib') (on the same library path where I am trying to install LDheatmap) installed.packages(lib='/home/sblay/lib') Package LibPath Version Priority Bundle combinat combinat /home/sblay/lib 0.0-5 NA NA gdata gdata /home/sblay/lib 2.0.0 NA gregmisc genetics genetics /home/sblay/lib 1.1.1 NA NA gmodels gmodels /home/sblay/lib 2.0.0 NA gregmisc gplotsgplots/home/sblay/lib 2.0.0 NA gregmisc gtoolsgtools/home/sblay/lib 2.0.0 NA gregmisc LDheatmap LDheatmap /home/sblay/lib 1.0 NA NA ... I am developing a package named LDehatmap. It depends on the genetics package and includes two data files and a demo file. When I'm trying to install it, I get the following messages: * Installing *source* package 'LDheatmap' ... ** R ** data ** demo ** help Building/Updating help pages for package 'LDheatmap' Formats: text html latex example LDheatmaptexthtmllatex example ldheatmaptexthtmllatex example Error: object 'reorder' not found whilst loading namespace 'gdata' Error: package 'gdata' could not be loaded Execution halted ERROR: installing package indices failed Any ideas? Yes. You do not have gdata (part of gregmisc) installed, and genetics depends on it. How did you get genetics installed? A binary install? Install gregmisc __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ERROR: installing package indices failed
Dear R-helpers, I am developing a package named LDehatmap. It depends on the genetics package and includes two data files and a demo file. When I'm trying to install it, I get the following messages: * Installing *source* package 'LDheatmap' ... ** R ** data ** demo ** help Building/Updating help pages for package 'LDheatmap' Formats: text html latex example LDheatmaptexthtmllatex example ldheatmaptexthtmllatex example Error: object 'reorder' not found whilst loading namespace 'gdata' Error: package 'gdata' could not be loaded Execution halted ERROR: installing package indices failed Any ideas? Thanks, Sigal __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] C function name garbled
On Tue, Sep 07, 2004 at 04:57:57PM -0400, Duncan Murdoch wrote:
On Tue, 7 Sep 2004 12:46:55 -0700, S Blay [EMAIL PROTECTED] wrote :
I wrote an R wrapper function (phylpro) around a C function
(Rphylpro).
The first time I'm running my function, it runs with no errors.
The second time I'm trying to run it, I get an error message
with the first argument to .Call garbled.
Set up:
dyn.load(Phylpro.so)
source(phylpro.R)
WinHalfWidth-30
permReps-10
breaks-c(548, 735, 832)
First call to phylpro succeeds:
b-phylpro(simulinfile, breaks, WinHalfWidth, permReps)
Second call to phylpro fails:
b-phylpro(simulinfile, breaks, WinHalfWidth, permReps)
Error in .Call(PSg\bBh\b, input_file =
as.character(input_file), breaks = as.integer(breaks), :
.Call function name not in load table
Check if my C function name is in load table:
is.loaded(Rphylpro)
[1] TRUE
Any ideas?
It looks to me as though your function is doing something to mess up
R's internal data. I'd try commenting out the whole body of the
function, then adding it back gradually to find which part causes the
trouble.
Duncan Murdoch
I followed your advice - looks like I need some kind of a cast
when I assign the values of a C vector to an R vector. I think.
Below is an example of something that doesn't work -
Can someone give me a hand?
(In the real function, there are also integer and Character
string C vectors...)
Thanks.
#include R.h
#include Rdefines.h
SEXP myfunc() {
double *corrs;
corrs[0]=3.0;
SEXP Rcorrs;
double *pRcorrs;
PROTECT(Rcorrs = NEW_NUMERIC(1));
pRcorrs = NUMERIC_POINTER(Rcorrs);
pRcorrs[0] = corrs[0];
UNPROTECT(1);
return(R_NilValue);
}
/*
dyn.load(myfunc.so)
func-function().Call(myfunc)
func()
*/
Run it once, it's ok:
func()
NULL
Run it twice, not ok:
func()
Error in .Call(NULL) : function name must be a string (of length 1)
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Re: [R] allocating memory in C, not in R
Below is a simplified version of my c function that I am
currenctly using with a .C() call.
The values that has to be returned to R are the three outVectors.
If I need to convert .C to .Call,
How do I do it based on myFunction below?
Thank you for your help.
void myFunction(char **argv, int *inputVector,
int *RoutVector1, double *RoutVector2, char **RoutVector3) {
int*outVector1;
double *outVector2;
char **outVector3;
int roof = 0;
roof = calculate_values ( argv[0],
inputVector,
outVector1,
outVector2,
outVector3 )
for(i=0;iroof;i++) {
RoutVector1[i] = outVector1[i];
RoutVector2[i] = outVector2[i];
}
return;
}
Well, you could read Writing R Extensions (Section 4.8). Your
function will have to change significantly, though. I would
create a list within the C-function (called val below) and
populate the RoutVectors with it.
(I can't remember whether you'll need more than #include R.h.
Again, I direct you to the documentation.)
SEXP myFunction(SEXP argv, SEXP inputVector) {
SEXP val;
PROTECT(val = allocVector(VECSXP, 3));
/* some code you'll have to write */
UNPROTECT(1);
return val;
}
# in R
RoutVectors - .Call(myFunction, argv, inputVector)
--sundar
Thanks Sundar - but how do I return several vector objects of
different modes wrapped in a list object using .Call?
Sigal
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Re: [R] allocating memory in C, not in R
Thank you for the fast reply.
Below is a simplified version of my c function that I am
currenctly using with a .C() call.
The values that has to be returned to R are the three outVectors.
If I need to convert .C to .Call,
How do I do it based on myFunction below?
Thank you for your help.
void myFunction(char **argv, int *inputVector,
int *RoutVector1, double *RoutVector2, char **RoutVector3) {
int*outVector1;
double *outVector2;
char **outVector3;
int roof = 0;
roof = calculate_values ( argv[0],
inputVector,
outVector1,
outVector2,
outVector3 )
for(i=0;iroof;i++) {
RoutVector1[i] = outVector1[i];
RoutVector2[i] = outVector2[i];
}
return;
}
On Wed, Sep 01, 2004 at 10:16:59PM +0100, Prof Brian Ripley wrote:
On Wed, 1 Sep 2004, S. Blay wrote:
I need to retrieve several vectors of various types from a call
to .C(), but I don't know their length in advance.
Is there a way to do this without allocating an excessive amount
of memory?
If so, an example would be very helpful.
It would be very much easier to use .Call rather than .C.
Alternatively, generate and allocate in C on one C call and retrieve on a
second, as rpart does.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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