similar to: Question about spatial statistics

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

Hi people, I have made some progress trying to work out how to solve this problem but I have got a bit stuck - sorry if this turns out to be a simple exercise . . Allelic Differentiation (AD) in genetics measures the number of different alleles between (say) two populations eg: Organisms in Pop 1 have alleles: a, b, c, d, e Organisms in Pop 2 have alleles: b, b, c, d, e Different

> 3x3 subset used > Locus1 Locus2 Locus3 > Samp1 GG <NA> GG > Samp2 AG CA GA > Samp3 AG CA GG > > The euclidean distance function is defined as: sqrt(sum((x_i - y_i)^2)) My > assumption was that the difference between

Dear, I am using the R package SNPRelate but I found an error when I run the following command. Do you know what might be the problem? Thanks in advance. > vcf.fn <- system.file("extdata","str.vcf",package="SNPRelate") > snpgdsVCF2GDS(vcf.fn,"test.gds") Start snpgdsVCF2GDS ... Extracting bi-allelic and polymorhpic SNPs.

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

Dear R developers: I am a PHD candidate student in the school of public health of Peking University and my major is genetic epidemiology. I am learning the FAM-MDR algorithm, which is used to detect the gene-gene and gene-environment interactions in the data of pedigree. The codes were written by Tom Cattaert of the University of Liege. The algorithms and the sample datasets are available at

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.

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().

I am about one step away from heaven on earth. I think only one step! I am using dgc.genetics to run a TDT test on thousands of genetic loci. I have learnt (through the help of others on this mailing list) to send the complex output to useful data frames which in turn allow me to look at the big picture and screen the thousands of loci. Resultdt<-lapply(PGWide[,240:290], tdt) the above

Hi all, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency.

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

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

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

Hi, I am looking for some code for Moran's I. Has anyone previously done this? I have been unable to find it in the search engines. James

i would like to perform moran's analysis with r... thanks duccio

Hi, I am trying to calculate Moran's I test for the residuals for a regression equation, but I have trouble converting my coordinates into nb format. I have used the dnearneigh() funtion now with an arbitrarily high upper distance to make it include all plots. However, when I do the lm.morantest() I get a Moran's I value which is the same as the expected value and a P-value of 1. I

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

I want to do "moran's I test" in R language. I try to use "gearymoran" in Package "ade4","moran" in Package "spdep", and Moran.I in Package "ape". But I do not know how to do it because data format is different. My data: x y dbh 111.03 10.7 7 118.11 0.28 1.2 165.36 0.36 8.4

Ape is an R package for "analyses of phylogenetics and evolution". The first version (0.1) has been released on 27 August 2002 and is available on CRAN. >From the 'Description' file of version 0.1: Ape provides functions for reading, and plotting phylogenetic trees in parenthetic format (standard Newick format), analyses of comparative data in a

I'm trying to use the package ARES to produce allelic richness estimates with extrapolation beyond the sample size. I've begun by testing the program with the butterfly_borneo data provided with the package, but I seem to be having a problem with the read.genepop function. Below, I've included my R code along with the error I receive after trying to read the genepop file. I'm