search for: genetics

Hi, I am trying to install the genetics package on a server with Linux, Fedora. I installed it in a PC and worked fine. In a server since I am not used with R, I am not sure what do I need to change so genetics pkg can see some package dependencies: Any suggestion is appreciated, Aldi Note: genetics expects gregmisc and mvtnorm to be...

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really...

Dear R-developers, I would appreciate any insights over compiling R 3.4 with Intel MKL -- I have been successful until R 3.3.3 but now it stops complaining about pcre though it worked without Intel MKL as follows, ./configure LDFLAGS=-L/genetics/data/software/lib CFLAGS=-fPIC -I/genetics/data/software/include --enable-R-shlib I have used, export MKL_NUM_THREADS=15 export MKLROOT=/genetics/data/software/intel/composer_xe_2013.4.183/mkl export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MKLROOT/lib/intel64 /genetics/data/software/intel/composer_xe...

...an.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -fopenmp -m64 -I/genetics/data/software/intel/composer_xe_2013.4.183/mkl/include -L/genetics/data/software/intel/composer_xe_2013.4.183/mkl/lib/intel64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lpthread -lm -lgfortran -lm -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm grep.o: In function `setup_jit': /genetics/dat...

Hi, I am doing some research on feature selection for classfication problem using genetic algorithm in a wrapper approach. I am wondering if there is some package which is already built for this purpose. I was advised before about dprep package but I don't think it used GA there (if I am wrong, please correct me!) Thanks, Ed

...ta analyst to work on projects with genetic data. Our computing environment is almost exclusively R and we have developed several R and BioConductor packages. Position Description: The Department of Biostatistics of the University of Washington, through the Center for Biomedical Statistics and the Genetics Coordinating Center, is engaging in an increasing number of analyses of genetic data, mainly from human population samples. These data sets include whole-genome sets of single nucleotide polymorphism data from microarrays and next-generation sequencing, as well as a variety of phenotypic traits of...

Dear R-users, I intend to do a spatial analysis on the genetic structuring within a population. For this I had thought to prepare a kernel density estimate map showing the spatial distribution of individuals, while incorporating the genetic distances among individuals. I have a dataset of locations of N unique individuals (XY-coordinates) and an NxN matrix with the genetic distances given as a

...patients by meta-analysis; inferring disease-causing molecular pathways from genotype, phenotypes, and omics profile of patient-derived cell lines (transcritptomic, proteomic and metabolic). The developed methods will be applied to data from our collaborator Dr. Holger Prokisch, Institute of Human Genetics of Munich (cellular respiratory disorders) and will lead to functional validation studies directly on cell lines derived from patients. The successful candidate will be part of SOUND, an international research project funded by the European Commission within its Horizon 2020 Research and Innovatio...

Dear Sir, We need to use genetics packages at our end. We have installed R packages. When i try to choose genetics package and install, it is giving an error. Please see the attachment for the error. How can i resolve it and make it work? Thanking you A Padmavathi Devi Technical Officer Centre for Cellular and Molecular Biology Ph...

Hi, I'm looking for a R-package that does feature selection for PLS using a genetic optimization algorithm. I couldn't find one on CRAN and I wonder whether there is a free one. I would be very appreciative for any help. Regards Rolf

mcga 1.1 (machine coded genetic algorithms) package implements a genetic algorithm optimisation tool with machine coded chromosomes. The machine coded chromosomes stand for chromosomes that are not decoded and encoded. The byte representation of 'double' type variables are crossed-over and mutated. This is different from the binary coded and real coded genetic algorithms. Linux and

mcga 1.1 (machine coded genetic algorithms) package implements a genetic algorithm optimisation tool with machine coded chromosomes. The machine coded chromosomes stand for chromosomes that are not decoded and encoded. The byte representation of 'double' type variables are crossed-over and mutated. This is different from the binary coded and real coded genetic algorithms. Linux and

Hi, I have a genotype data for both case and controls and would like to calculate the HW p-value. However, since the number of one genotype is 0, I got wired result. Would someone help me to figure it out? Or confirm it's right? Thanks a lot. ============ > library( "genetics" ) NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for informtion. > case.data <- c("G/G","G/G","G/G&quot...

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: te...

I am aware of the R Genetics Project that developed the R library and software called Bioconductor (http://www.bioconductor.org/ ) . How do the two relate to each other? What is the one that the other is not and vice versa? Can anybody link me to something that answers the question? -- Farrel Buchinsky, MD Pediatric Otola...

Hi All, I've been working on updating the 'genetics' package. As a consequence of the upgrade, .First.lib() looks like: .First.lib <- function(libname, pkgname) { if (!require(combinat)) warning("Unable to load 'combinat' library. Function `diseq.ci' will fail.") require(gregmisc) genotype...

...ic toxicology study where I artificially fertilized and exposed embryos to a chemical and counted defects. In addition, I kept track of male-female pairs that I used to artificially fertilize and generate embryos with. I need to use logistic regression to model the response, but also check that the genetics of the pairings did or did not have an effect on the response. My data looks a bit like this: response matrix chemical concentration Genetic Matrix Present Absent Male Female 2 152 0.13 a 1 6 121 1 a 2 21 92...

Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work > summary(founders[,59]) to prove that it is a genotype class > class(founders[,59]) [1] "genotype" "factor" Now when I issue the command: > summary(founders[,59]) I get: Error in attr(retval,...

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 includ...

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 includ...