similar to: Haplotype network appearance

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

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

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

Hi all, I am working for reconstructing haplotype from individual's SNPs. But I have met a problem that most of paper and software I found are focus on reconstructing haplotype from population's SNPs, rather than individual's SNPs. I wonder is there any R package can be used to solve such problem? Thanks in advance for any information, Gang Chen [[alternative HTML version

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

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]]

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

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

Hi, For the last few days I have tried utilise your package "pegas" in order to obtain some values for indices like the nuclear diversity and tajimas d value. I have modified my dataset (a text file containing dna sequences) in order to be able to read it in with the tools provided by pegas. Here, I have oriented myself on the description provided by the help-page in read.loci().

Hi! I am trying to analyse my data using amova (http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova): My input to R is a DNA sequence file, format=fasta dna<- read.dna("XX.fasta", format="fasta") #left other options as default d<- dist.dna(dna, model="raw") g<- read.table("XXX.design") Load necessary libraries: library(pegas)

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"),

Hi Ana, I have exactly the same problem as you! Anyone can help us? Thanks in advance, Nuria >Hello all! > >I'm using Samba 2.2.1-a4 on Red Hat 7.1 as PDC. Everything is working >fine but 2 issues: > >1. When accesing shares on Win98 system from Network Neighborhood on a >NT wks, I get an Access Denied message when double-clicking the Win98 >box. >I can map

Dear friends, I would like to announce for tests and free use a good add-on for Samba. It is a LAN-based interface for famous Pegasus Mail by David Harris, emulating his Mercury MTA. Note that this message have passed through this system. Look in headers. It is working! http://www.cor.neva.ru/~aal/pegas/pegas+qmail-1_0.tar.gz (7k) The file contains the patch against qmail 1.03, source of

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

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

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

Monty, Thanks for writing up your thoughts on the mux design (ogg/doc/ogg-multiplex.html in cvs) Now that there's something to argue with, I'd like to comment. To recap, the documented proposal is that we make two categories of streams within the OggFile multiplexing library. Pages are sorted chronologically by the timestamp equivalent of their granulepos fields. Normal data like

Hi, I'm trying to fit some data using a logistic function defined as y ~ a * (1+m*exp(-x/tau)) / (1+n*exp(-x/tau) My data is below: x <- 1:100 y <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,1,1,1,2,2,2,2,2,3,4,4,4,5, 5,5,5,6,6,6,6,6,8,8,9,9,10,13,14,16,19,21, 24,28,33,40,42,44,50,54,69,70,93,96,110,127,127,141,157,169,

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

Hi AlL, I ahve this problem that my objective function is discontinous in the paramaters and I need to use methods such as nelder-mead to get around this. My question is: How do i compute standard errors to a problem that does not have a gradient? Any literature on this is greatly appreciated. Jean,