search for: 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 references are not provided. Does anybody knows how it...

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 acros...

Hi , is it possible to calculate ld-measures D, D', r and perhaps corresponding p-values with r IF THE PHASE IS KNOWN? The genetics - package provides the LD function only for ambigious phase. Thank you very much Bettina Kulle

...NA Genotype Frequency: Count Proportion 1/1 26 0.5 1/2 21 0.4 2/2 5 0.1 NA 20 NA Heterozygosity (Hu) = 0.4225168 Poly. Inf. Content = 0.3309022 tdt(Genotype.914186, MessWith, famid, pid, fatid, motid, sex, affected ) Transmission/disequilibrium test Data: Genotype.914186 Untransmitted allele frequencies, informative transmissions and exact P-values Allele Frequency Transmitted Untransmitted P-value 2 0.3333 3 2 1.000 trio.types(Genotype.914186, MessWith, famid, p...

...nd 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 out the LDheatmap() package which can generate the plots you describe. The help indicates that it accepts a matrix of pair-wise linkage disequilibrium measures, one of which is R^2 (the correlation coefficient between loci), but I suspect you could simply pass it a matrix of correlation coefficents. Hope that helps, Neil -- "In mathematics you don't understand things. You just get used to them." - Johann von Neumann Email - nsh...

Hello, I am having really hard time finding a good article about simulating genotypes of cases and controls at a disease locus using R. if you guys can point me or guide me where i can find more information, it will be helpful. thanks, Claire -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17065607.html Sent from the R help mailing list archive at

...nd also for taking your time to answer my question. Dear Frank, I'm a PhD student of animal breeding science from Iran. Unfortunately although I try more time for running your package in order to simulate of a historical and reference population based on hypred manual (step by step) but linkage disequilibrium (LD) value was true (near 0.20) only when the generations was less than 50. In other words when I try for more generations this value increased subsequently. If it is possible please help me and let me know how should I change your program for getting near true value of LD when generation increased...

Dear useRs, First off, sorry about the long post. Figured it's better to give context to get good answers (I hope!). Some time ago I wrote an R function that will get all pairwise interactions of variables in a data frame. This worked fine at the time, but now a colleague would like me to do this with a much larger dataset. They don't know how many variables they are going to have in the

CRAN (and crantastic) updates this week New packages ------------ * disclapmix (0.1) Maintainer: Mikkel Meyer Andersen Author(s): Mikkel Meyer Andersen and Poul Svante Eriksen License: GPL-2 http://crantastic.org/packages/disclapmix disclapmix makes inference in a mixture of Discrete Laplace distributions using the EM algorithm. * EstSimPDMP (1.1) Maintainer: Unknown Author(s):