search for: pedigree

Hi Im using the kinship package to draw a pedigree. On my data set this works fine but when i add indivudals to the pedigree i keep getting an error i hope someone can help me! This is the code im using: Data<-read.table("Tree.txt", header=T, sep=",") attach(Data) ped<-pedigree(id, dadid, momid, sex, aff) par(xpd=T) plot...

I wish to make modifications to the plot.pedigree function in the kinship package. My attempts to contact the maintainer have been unsuccessful, but my question is general, so specifics of the kinship package might not be an issue. My first attempt was to make a new function Plot.pedigree in the .GlobalEnv which mostly achieved what I wanted to....

Hello, I am using the Kinship package to draw a pedigree plot. I am trying to control the spacing between individuals in the pedigree. Currently, it is drawing a pedigree with too little space, so the text is overlapping. I'd like to increase the distance between individuals. According to the documentation, I would expect the following to be relev...

...out 10,000 animals in our colony. I am interested in graphing simple family trees for a given subject or small number of subjects. The basic idea is: start with data frame from entire colony and list of index animals. I need to identify all immediate relatives of these index animals and plot the pedigree for them. We're not trying to do any sort of real analysis, just present a visualization of the family structure. I have used the kinship and pedigree packages to plot the pedigree. My question relates to efficiently identifying the animals to include in the pedigree: Starting with the data...

...t;, "46", "47", "48", "49", "50", "51", "52", "53", "54", "55"), class = "data.frame")) d estoy interesado en obtener un archivo de texto "out.txt" con la siguiente estructura: pedigree: 1 ped id father mother sex affected 1 1 2 3 2 1 1 2 0 0 1 2 1 3 0 0 2 1 1 4 2 3 2 1 1 5 2 3 2 2 1 6 2 3 1 2 1 7 2 3 2 2 pedigree: 2 ped id fath...

Hola a todos, me gustaría realizar una consulta asociada a la generación de valores genéticos del pedigreemm en R. Primero generé el archivo de pedigree incluyendo los parentales para posteriormente estimar la varianza aditiva y los valores genéticos para cada individuo, relacionando los individuos por medio de la matriz de parentesco. Me da todo perfecto, el complemento pedigreemm trabaja muy bien,...

...installing DLL installing R files installing man source files installing indices installing help >>> Building/Updating help pages for package 'GeneticsPed' Formats: text html latex example chm NAtoUnknown text html latex example code.pedigree text html latex example extend.pedigree text html latex example generate.pedigree text html latex example generation text html latex example getcode.pedigree text...

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 http://www.statgen.ulg.ac.be/index.php?option=com_content&view=article&id=90&Itemid=85. The R I used is R-2.15.1 in the Windows XP system. The command lines I...

Dear useRs: Announcing the release of kinship2, version 1.2.1, to CRAN. kinship2 is a branch from the original kinship package with some key updates for the pedigree and kinship functions, with some additional functions that work with the pedigree object. Highlights: * pedigree and pedigreeList objects implemented with S3 methods print and "[," * pedigree plotting routine re-written, now more robust * kinship matrices now implemented with Matrix p...

Dear useRs: Announcing the release of kinship2, version 1.2.1, to CRAN. kinship2 is a branch from the original kinship package with some key updates for the pedigree and kinship functions, with some additional functions that work with the pedigree object. Highlights: * pedigree and pedigreeList objects implemented with S3 methods print and "[," * pedigree plotting routine re-written, now more robust * kinship matrices now implemented with Matrix p...

Dear all, I'd like to introduce the paramlink package, offering parametric linkage analysis in R, as well as other likelihood-based pedigree analyses. While a rudimentary version of the package has existed for a while, it was never properly introduced to this forum. The present version is a major update with new and improved functions. Features: * Singlepoint LOD scores for simple/complex/inbred pedigrees (implementing the E...

Dear all, I'd like to introduce the paramlink package, offering parametric linkage analysis in R, as well as other likelihood-based pedigree analyses. While a rudimentary version of the package has existed for a while, it was never properly introduced to this forum. The present version is a major update with new and improved functions. Features: * Singlepoint LOD scores for simple/complex/inbred pedigrees (implementing the E...

I'm currently packaging up some of the kinship matrix routines more formally, these are used in coxme when dealing with family correlation structures. One of my test programs exercises error conditions, i.e., it purposely feeds particular types of invalid pedigree data in to see if the right error message results. So there are comment-action pairs # the next line should generate a "pedigree loop" error kindepth(..... As I found out last night, such tests case a failure of R CMD check! Any suggestions on how to properly package these? A second...

...miological analysis. Could you please confirm which of these (or others) would be most suitable for our needs? Dietary Intake/Analysis: We are considering packages like foodfreq and Dietary for dietary intake analysis. Are these the best options, or do you recommend other packages for this purpose? Pedigree Analysis: We are exploring the kinship2 and pedigree packages for pedigree data analysis. Is there a package you would suggest for more comprehensive analysis? Migration-Related Study: We are interested in migration-related studies and have identified the migrant and spatstat packages. Would these...

...d you please confirm which > of these (or others) would be most suitable for our needs? > Dietary Intake/Analysis: We are considering packages like foodfreq and > Dietary for dietary intake analysis. Are these the best options, or do you > recommend other packages for this purpose? > Pedigree Analysis: We are exploring the kinship2 and pedigree packages for > pedigree data analysis. Is there a package you would suggest for more > comprehensive analysis? > Migration-Related Study: We are interested in migration-related studies and > have identified the migrant and spatstat pa...

Hi, I have a dataframe that contains pedigree information; that is individual, sire and dam identities as separate columns. It also has date of birth. These identifiers are not numeric, or not sequential. Obviously, an identifier can appear in one or two columns, depending on whether it was a parent or not. These should be consistent. Not a...

...Subject: [R] animal models and lme > > > > -- > Hi R users, > > I'm trying to fit an animal model using lme and cannot fit the > corelation matrix which describes the additive genetic correlation > between individuals. > > I have created a test data set (pedigree) where the first column > specifies the id of each individual, and the second column contains > simulated trait values. AGRM is the corresponding additive genetic > relationship matrix whose elements are equal to the genetic > correlation between individuals. > > The test dat...

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 is the name or id of the locus. I am able to get the tdt to run by each locu...

Ron Crump wrote: > Hi, > > I have a dataframe that contains pedigree information; > that is individual, sire and dam identities as separate > columns. It also has date of birth. > > These identifiers are not numeric, or not sequential. > > Obviously, an identifier can appear in one or two columns, > depending on whether it was a parent or not....

Hi All, I'd like to ask for a few clarifications. I am doing some calculations over some biggish datasets. One has ~ 23000 rows, and 6 columns, the other has ~620000 rows and 6 columns. I am using these datasets to perform a simulation of of haplotype coalescence over a pedigree (the datestes themselves are pedigree information). I created a new dataset (same number of rows as the pedigree dataset, 2 colums) and I use a looping functions to assign haplotypes according to a standrd biological reprodictive process (i.e. meiosis, sexual reproduction). My code is someting lik...