Displaying 20 results from an estimated 800 matches similar to: "Version 1.0 of hapassoc now available from CRAN"
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2008 Sep 19
2
Extract method for a new class
Dear list,
I am trying to write a package for simulating meioses in R. We defined a class 'haplotype' which contains the basic units of our simulation:
setClass("haplotype",representation(snp = "numeric",qtl = "list",
hID = "numeric",phID0 = "numeric",phID1 = "numeric"),
2004 Nov 19
2
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
2006 Mar 16
1
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
2009 Jan 22
1
infer haplotypes phasing trios tdthap
Dear R mailing list,
I have a dataset with genotypes from trios and I would like to infer
haplotypes for each mother, father and child. The package that I could
find that can do this is tdthap.
But when the mother is homozygous (e.g., 2/2) the haplotype is called as
not possible to infer (0); I would prefer for it to call the genotype
(2). From what I understand it is doing what I would like
2002 Sep 14
0
R-version of haplo.score uploaded to CRAN
I've just uploaded an R version of Daniel Schaid's 'haplo.score' library
(from http://www.mayo.edu/statgen/) to CRAN.
>From the DESCRIPTION file:
[haplo.score is a] suite of routines that can be used to compute score
statistics to test associations between haplotypes and a wide variety of
traits, including binary, ordinal, quantitative, and Poisson. These methods
assume
2009 Jun 02
1
C++ to R : 64bit to 32bit problem.
Hi,
I'm new to calling C++/C programs from R and am having some trouble getting
started. Following Sigal Blay (Simon Fraser University)'s instructions, I
have a .c file called "useC1.c":
/* useC1.c */
void useC(int *i) {
i[0] = 11;
}
This produces a .o file : "useC1.o" in a specified directory. I then open
R, set the proper directory and:
2010 May 01
3
Resize Graphics Window
Need way to resize an existing graphics window.
This should be applicable across platforms (as part of a package).
Context: function1() draws main plot (I'm using grid), function2() adds smaller plot
above main plot, but this one can sometimes overflow the original graphics window
area.
Thanks,
Sigal
2009 Oct 20
1
how to draw stacked ellipses to illustrate the shared and specific of multiple objects using R
Dear R-help listers,
I am now asking for helps on how to draw stacked ellipses to
illustrate the shared and specific of multiple objects using R.
My problem comes from my population genetics study. Now, I genotyped
three species, and I get known about the amount of shared and specific
haplotypes in each of the species and their combinations. I want to
illustrate this result in three stack
2009 Aug 31
1
permutation test - query
Hi,
My query is regarding permutation test and reshuffling of genotype/phenotype
data
I have been using the haplo.stats package of R. for haplotype analysis and I
would like to perform an analysis which I'm requesting your advice.
I have a data set of individuals genotyped for 12 SNP and a dichotomous
phenotype.
At first, I have tested each of those SNP independently in order to bypass
2007 Jul 23
1
(no subject)
Dear Sir/Madam,
I am running a R program for my SNP data. There are some errors when I run
glm model in Hapassoc software, sometimes it is over the memory and
sometimes the matrix is singular. I want to ingore these errors and excute
the next statement. Otherwise, I have a big big trouble. Do you have some
idea about this problem of ingore errors.
Wish to get your help assp.
thanks.
--
Wei
2006 Mar 24
1
cox model for haplotypes
Hi,
Anybody knows a function that can fit haplotype data to a Cox model.
I've been searching it in the web without succeed.
I use "haplo.stats" package, but unfortunatelly it's not possible to
analyse survival data, amb I right?.
Thanks in advance.
Isaac Subirana (isubirana@imim.es)
[[alternative HTML version deleted]]
2007 May 25
1
Speeding up resampling of rows from a large matrix
I'm trying to:
Resample with replacement pairs of distinct rows from a 120 x 65,000
matrix H of 0's and 1's. For each resampled pair sum the resulting 2
x 65,000 matrix by column:
0 1 0 1 ...
+
0 0 1 1 ...
_______
= 0 1 1 2 ...
For each column accumulate the number of 0's, 1's and 2's over the
resamples to obtain a 3 x 65,000 matrix G.
For those
2005 Jul 01
2
loop over large dataset
Hi All,
I'd like to ask for a few clarifications. I am doing some calculations
over some biggish datasets. One has ~ 23000 rows, and 6 columns, the
other has ~620000 rows and 6 columns.
I am using these datasets to perform a simulation of of haplotype
coalescence over a pedigree (the datestes themselves are pedigree
information). I created a new dataset (same number of rows as the
pedigree
2006 Mar 12
0
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
2011 Jan 12
0
adonis, amova and haplotype frequency
Dear All,
I'd like to perform adonis (from the vegan package) rather than amova
(in ade4) on some haplotype data, as I have crossed factors. Is there a
simple way to tweak the source to allow weights (haplotype frequencies)
in a similar way to amova?
Best
Simon
2010 Nov 09
0
haplotype and epistasis analysis using 3 or more SNPs?
Dear Mme/Mr.
Hope you are doing well. I am doing some genetic analysis using The R software and I have difficulties to find how I can perform an Interaction/epistasis analysis using 3 or more SNPs (=markers) ? (In the instructive manual, there is only an interaction/epistasis analysis with 2 markers).
In addition can you please inform me how I can perform Haplotype analysis and if there is an
2012 Jan 10
0
haplo.stats version 1.5.2
haplo.stats, version 1.5.2, is now available on CRAN.
Below I provide the description and link to our software page where you
can also find the updated user manual. The most notable updates for this
version were to make the haplo.glm fitted object work more like the glm
object; other changes are listed in the NEWS file entries pasted below.
DESCRIPTION:
haplo.stats: Statistical Analysis of
2012 Jan 10
0
haplo.stats version 1.5.2
haplo.stats, version 1.5.2, is now available on CRAN.
Below I provide the description and link to our software page where you
can also find the updated user manual. The most notable updates for this
version were to make the haplo.glm fitted object work more like the glm
object; other changes are listed in the NEWS file entries pasted below.
DESCRIPTION:
haplo.stats: Statistical Analysis of