similar to: EM algorithm for multiple-locus haplotypes frequencies

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]]

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

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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

Dear all, To draw a lowess line on a plot was a piece of cake; to draw a loess line, however, seems not that easy. Is the loess plotting implemented at all in relation to the loess function, or do I have to look in add-on packages? Thanks, Marcin

Hi, Consider this simple plot: > plot(1:25,runif(25,0,1),ylab="First Y-axis label",xaxt="n") I want to add an additional axis as > axis(4,at=seq(0.2,1,.2), labels=1:5) I have no idea how to add now the title of the new axis as "Second Y-axis label". I want this text to be vertically directed from bottom to top. I can't find the function in text() to write

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

Hi, I want to add boxplots to a scatterplot: plot(x,y, xlim=c(80,120),ylim=c(80,120)) boxplot(y,add=TRUE,at=118) boxplot(x,add=TRUE,at=118,horizontal=TRUE) How can I control the width of the boxes (say, I'd like them to be of width 3 in the variables' scales). I've tried the "width" parameter but failed. Thanks in advance, Marcin

Hi All, is there any chance of vectorising the two ifelse() statements in the following code: for(i in gp){ new[i,1] = 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

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here:

I see something new and unexpected here. > update.packages() trying URL `http://cran.r-project.org/src/contrib/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 163467 bytes opened URL .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ......... downloaded

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which

haplo.stats, version 1.5.2, is now available on CRAN. Below I provide the description and link 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

haplo.stats, version 1.5.2, is now available on CRAN. Below I provide the description and link 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

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

Hi, I am clustering objects using the agnes() function and the UPGMA clustering method (function = "average"). Everything works well, but apparently something is wrong with the dendrogram. For example: x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3) y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115) xy<-cbind(x,y) library(cluster) UPGMA.orig<-agnes(x)

Dear all, Considering this simple example of hexbinplot: mixdata <- data.frame(x = c(rnorm(5000), rnorm(5000,4,1.5)), y = c(rnorm(5000), rnorm(5000,2,3)), a = gl(2, 5000)) fig <- hexbinplot(y ~ x | a, mixdata) print(fig) update(fig, colramp = BTC) produces a bad (non-updated) legend. Compare it with: hexbinplot(y ~ x | a, mixdata, colramp = BTC) What

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

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"),