similar to: calculating of linkage-disequilibrium measures?

hi, i am not able to extract the p-values from the Manova function in the car library. I need to use this function in a high-throughput setting and somehow need the p-values produced. Any ideas? Best regards Bettina Kulle Andreassen -- Bettina Kulle Andreassen University of Oslo Department of Biostatistics and Institute for Epi-Gen (Faculty Division Ahus) tel: +47 22851193 +47 67963923

hi, i am getting an error when calling the impute.knn function (see the screenshot below). what is the problem here and how can it be solved? screenshot: ################## *** caught segfault *** address 0x513c7b84, cause 'memory not mapped' Traceback: 1: .Fortran("knnimp", x, ximp = x, p, n, imiss = imiss, irmiss, as.integer(k), double(p), double(n), integer(p),

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

# Hello, # I have a list with 6 categories and with different numbers of rows. # I would like to change each of them into a unique data frame in order to match # values with other data frames and perform some calculations. # Or I could make each category or list element have the same number of rows and create one large data.frame. # below is a creation of a sample list # I apologize for the

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 lists, I want to construct a loop in R, but don't know how to do it. I can do it in SAS, but I prefer in R (which I am hoping I will off SAS for good soon). Could anyone help me to convert the SAS codes to equivalent R codes. Basically, the following codes were written to establish the sire gametes or phases for daughter design for one markers two alleles. Here are the SAS code: do

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

#If I have two lists as follows a1<- array(1:6, dim=c(2,3)) a2<- array(7:12, dim=c(2,3)) l1<- list(a1,a2) a3<- array(1:4, dim=c(2,2)) a4<- array(5:8, dim=c(2,2)) l2<- list(a3,a4) #how can I create a new list with the mean across all arrays within the list, so all components are included? As an example for [[1]]; cbind((l1[[1]][,1]+l2[[1]][,1])/2,

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

Hello R-help community, I have another question about filtering datasets. Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

I'm sorry everyone for the inconvenience of spamming the R-help... Here's the complete post: Hi everyone, > > Since it's quite a while that I used the reshape package, I now feel kind > of rusty. > > I have a data.frame like this: > > > > id Sample.Name Marker Allele.1 > Allele.2 sample_id species

Hello, I have a dataset with proportions that vary around a fixed mean, is it possible to use betareg to look at variance in the dispersion parameter while keeping the mean fixed? I am very new to R but have tried the following: svec<-c(qlogis(mean(data1$scaled)),0,0,0) f<-betareg(scaled~-1 | expt_label + grouped_hpi, data=data1, link.phi="log",

Hello All, Once again thanks for all of the help to date. I am climbing my R learning curve. I've got a few more questions that I hope I can get some guidance on though. I am not sure whether the etiquette is to break up multiple questions or not but I'll keep them together here for now as it may help put the questions in context despite the fact that the post may get a little long.

Hello, I have a data-frame in which one-column is a factor: > str(data); `data.frame': 194 obs. of 8 variables: $ Type : Factor w/ 3 levels "Nuclear-Rec..",..: 1 2 2 2 2 2 2 2 2 2 ... $ Locus : num 0.000571 0.004000 0.001429 0.004857 0.007429 ... And I'd like to make a boxplot of the data$Locus values, where each level of the factor gets its own

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

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:

My data looks like this: > data name G_hat_0_0 G_hat_1_0 G_hat_2_0 G_0 G_hat_0_1 G_hat_1_1 G_hat_2_1 G_1 1 rs0 0.488000 0.448625 0.063375 1 0.480875 0.454500 0.064625 1 2 rs1 0.002375 0.955375 0.042250 1 0.000000 0.062875 0.937125 2 3 rs2 0.050375 0.835875 0.113750 1 0.877250 0.115875 0.006875 0 4 rs3 0.000000 0.074750 0.925250 2 0.897750 0.102000

Dear list, I came across the following error for three of my newly written Rd-files: non-ASCII input and no declared encoding I can't make sense of this. Below I copied in one of the three files. Can anybody please tell me what's wrong with it? Thank you, Christian \name{tetragonula} \alias{tetragonula} \alias{tetragonula.coord} \docType{data} % \non_function{} \title{Microsatellite

I am using 'tm' package for text mining and facing an issue with finding the frequently occuring terms. From the definition it appears that findFreqTerms and minDocFreq are equivalent commands and both tries to identify the documents with terms appearing more than a specified threshold. However, I am getting drastically different results with both. I have given the results from both the