search for: haplotyp

Displaying 20 results from an estimated 36 matches for "haplotyp".

Did you mean: haplotype
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]...
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...
2008 Apr 11
1
EM algorithm for multiple-locus haplotypes frequencies
Hi all, I've been looking in R for an EM algorithm adjusted for multiple-locus haplotypes frequencies, but failed in 100%. Has anyone heard of anything of this kind in R? Thanks in advance, Marcin
2006 Apr 18
0
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 additi...
2006 Apr 18
0
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 additi...
2008 Apr 02
0
Is there any package can be used to solve individual haplotyping problem?
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 informatio...
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?
...c 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 option for the haplotype interaction? Thanks in advance and best regards, Fathalli ferid MD.
2017 Oct 27
1
genetics: backward haplotype transmission association algorithm
...aking 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 algorithm (BHTA) first described by the authors in Hum Hered 2002; 53: 197-215. I wonder whether the algorithm has been implemented in R - primarily I ask since I fail to understand exactly how the algorithm works and thought R code would help there. All best wishes...
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"),...
2016 Apr 26
0
Haplotype network appearance
Hi, I'm doing haplotype networks with the package pegas and the script from Jimmy O'Donell's blog. The networks which I obtain are a little ugly and I'd like to change some aspects of their appearance, but I'm just starting with R and I don't know how to do it. I have the following problems: -Some no...
2003 Feb 14
1
programs for genetics - haplo.score for R
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2005 Jul 21
3
vectorising ifelse()
...(srow[i]>0, new[srow[i],zippo[i]], sample(1:100, 1, prob =Y1, rep = T)) new[i,2] = ifelse(drow[i]>0, new[drow[i]>0,zappo[i]], sample(1:100, 1, prob =Y1, rep = T)) } Where I am forced to check if the value of drow and srow are >0 for each line... in practical terms, I am attributing haplotypes to a pedigree, so I have to give the haplotypes to the parents before I give them to the offspring. The vectors *zippo* and *zappo* are the chances of getting one or the other hap from the sire and dam respectively. *gp* is the vectors of non-ancestral animals. *new* is a two col matrix where the...
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 that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The methods provide several different global and haplotype-specific tes...
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 ellipses, with the shared and unique area of the stack ellipses were annotated with the relative amount. my data is as followed: ------------------------------------------------------------ hap.type...
2002 Nov 27
0
R genetics package now available
...inary 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 (unordered allele pairs) and haplotypes (ordered allele pairs). Genotypes and haplotypes can be annotated with chromosome, locus, gene, and marker information. Utility functions compute genotype and allele frequencies, flag homozygotes or heterozygotes, flag allele carriers of certain alleles, count the number of a specific allele car...
2002 Nov 27
0
R genetics package now available
...inary 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 (unordered allele pairs) and haplotypes (ordered allele pairs). Genotypes and haplotypes can be annotated with chromosome, locus, gene, and marker information. Utility functions compute genotype and allele frequencies, flag homozygotes or heterozygotes, flag allele carriers of certain alleles, count the number of a specific allele car...
2012 Jan 10
0
haplo.stats version 1.5.2
...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 Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous A suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main fu...
2012 Jan 10
0
haplo.stats version 1.5.2
...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 Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous A suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main fu...
2005 Aug 04
1
linkage disequilibrium
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