similar to: [R-pkgs] R package hypred: Simulation of genomic data in applied genetics

Dear useRs, I am glad to announce that the new R package "hypred", initial version 0.1, is now available on CRAN. "hypred" is a package for simulating high-density SNP data. Its main function, "hypredRecombine" is intended to be used as a "Software tool" in larger programs that simulate complex populations. The focus of the package is on producing

Dear useRs, I am glad to announce that the new R package "hypred", initial version 0.1, is now available on CRAN. "hypred" is a package for simulating high-density SNP data. Its main function, "hypredRecombine" is intended to be used as a "Software tool" in larger programs that simulate complex populations. The focus of the package is on producing

Does anyone know if the sib TDT has been implemented in R 1. Spielman, R.S., and Ewens, W.J. (1998) A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet 62, 450-458 -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

Dear R helpers, I am trying to test for linkage disequilibrium (LD) in R between all pairs of loci. Importantly, my loci are microsatellites and have up to 30 alleles per locus. Do you know of any R packages that can either (1) calculate measures of LD directly or (2) test for the presence of LD within a statistical framework? Every package I have run across seems to be only able to handle

Dear all, I'm using the package "Genetics", and I'm interested in the computation of D' statistics for Linkage Disequilibrium, for which the LD() command has been realised. Unfortunately I don't find any reference on "how" the D' is computed by the LD() function. In the package documentation it is generally referred as "MLE" estimation, but

> I am trying to produce a heatmap of pairwise correlations, but since the matrix is > symmetric, I only need either the upper or the lower triangle. I have scoured the > web and R documentation, but I have not been able to find a way to produce such a > figure. Is there a simple way to produce a heat map with only the part above or > below the diagonal? You might want to check

I am involved in a study where, as in most of life, men demonstrate themselves to be recalcitrant. So while we have many probands and most of their mothers we only have about 50% of the trios being complete. I have been running tdt and trio.types. It appears as if it is ignoring the duos. Sometimes a duo can be informative. For instance Father ..missing Mother 1/2 Proband 1/1 This duo shows that

Hi, is there any package/function in Bioconductor that can do this: if given the chromosome positions of a fragment, find out all genes within, and with the information about which strand is the sense strand. And vice versa. Thanks a lot. ----- Appreciate your time & attention! -- View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html

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Dear friends - a couple of papers in PNAS (lastly:framework for making better predictions by directly estimating variables' predictivity, Lo et al PNAS 2016; 113:14277-14282) have focused interest on mapping complex traits to multiple loci spread all over the genome. I have been around on the relevant taskview(s) I hope but fail to see that the backward haplotype transmission association

Please do NOT contact me for this post. Please see below for contact details. The company offers solutions for the secure storage and analysis of patient genome sequence information to enable its effective, confidential application to personalized healthcare. The jobholder will be involved in clinical next generation sequence (NGS) data analysis pipeline development. The candidates will be

Version 1.1.0 of the genetics package is now available on CRAN. This release adds namespace support, and several minor bug fixes. -Greg Gregory R. Warnes Manager, Non-Clinical Statistics Pfizer Global Research and Development LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}} _______________________________________________ R-packages mailing list R-packages at

Hello, Can anybody tell me what the format of the input data file should be for this R function? Poor package documentation. Thanks, Matt ******************************************************** Matthew D. MacManes PhD Student UC- Berkeley Department of Integrative Biology Museum of Vertebrate Zoology 3101 VLSB #3140 Berkeley, CA 94720 (510)642-7782 EMAIL: macmanes@berkeley.edu WEBSITE:

Version 1.1.0 of the genetics package is now available on CRAN. This release adds namespace support, and several minor bug fixes. -Greg Gregory R. Warnes Manager, Non-Clinical Statistics Pfizer Global Research and Development LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}} _______________________________________________ R-packages mailing list R-packages at

Dear all, we seek a talented and motivated post-doc to develop computational methods for inferring the molecular basis of genetic diseases by integration of personal omics data. Research topics include: identifying causal mutations of rare disease patients by meta-analysis; inferring disease-causing molecular pathways from genotype, phenotypes, and omics profile of patient-derived cell lines

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 Otolaryngologist Allegheny General Hospital Pittsburgh, PA

Great R people, I have noticed a strange behaviour in read.delim() and friends in the R 2.7.0 version. I will describe you the problem and also the solution I already found, just to be sure it is an expected behaviour and also to tell people, who may experience the same difficulty, a way to overcome it. And also to see if it is a proper behaviour or maybe a correction is needed. Here is the

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 so broad field that I belive one person

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, "which") <- which :

Our group in the Biostatistics Department at the University of Washington is currently seeking a data 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