similar to: Extracting data from .zip file in WINDOWS version of package

I have a data frame containing the Id, Mother, Father and Sex from about 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

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

Hola a todos, A partir de los siguientes datos: d <- list(`1` = structure(list(ped = c(1L, 1L, 1L, 1L, 1L, 1L, 1L), id = 1:7, father = c(2L, 0L, 0L, 2L, 2L, 2L, 2L), mother = c(3L, 0L, 0L, 3L, 3L, 3L, 3L), sex = c(2L, 1L, 2L, 2L, 2L, 1L, 2L), affected = c(1L, 2L, 1L, 1L, 2L, 2L, 2L)), row.names = c("1", "2", "3", "4", "5",

I am making the question clear. Please help. > Dear R experts > > I was using kinship package to fit mixed model with kinship matrix. > The package looks like lme4, but I could find a way to extract p-value > out of it. I need to extract is as I need to analyse large number of > variables (> 10000). > > Please help me: > > require(kinship) > > #Generating

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.pedigree(ped) This is my data looks like

Dear R-devel members, We are building a new package (GeneticsBase) for analysis of genetic data . While doing "R CMD check with R-2.1.1, I am getting the following error: ** building package indices ... Error in "colnames<-"(`*tmp*`, value = c("family", "pid", "father", "mother", : length of 'dimnames' [2] not equal to

Dear developeRs, I've searched the documentation, FAQ, and mailing lists, but haven't found the answer(*) to the following: When should one specify LazyLoad, LazyData, and ZipData? And what is the default if they are left unspecified? (*)Except that 1) If the package you are writing uses the methods package, specify LazyLoad: yes, and 2) The optional ZipData field controls whether the

Hello R experts, what follows is my reproducible example: mydata<-structure(list(ped.avg = c(335.9, 110.8, 645.7, 638.9, 1468.1, 126.4, 4811.1, 88.5, 868.5, 656.6, 723.6, 654, 2.8, 15, 14.2, 17.5, 15.4, 112.1, 424.7, 18.3, 19.9, 28.6, 25.6, 23.5, 15.4, 27, 62.1, 15.6, 74.6), ped.erst = c(96, 53.2, 615.2, 616.5, 512.9, 56.2, 1851.8, 57.1, 579.5, 613.2, 601.1, 613.6, 1.3, 6.3, 6.5, 6.1,

Dear R-experts Execuse me for an easy question, but I need help, sorry for that. >From days I have been working with a large dataset, where operations are needed within a component of dataset. Here is my question: I have big dataset where x1:.....x1000 or so. What I need to do is to work on 4 consequite variables to calculate a statistics and output. So far so good. There are more vector

Dear R-helpers, First I apologize if my question is quite simple I have a large datasets which more 100 variables. For a research I need to change all name of variables with add one or more letters on each variables. For example, > data(Pima.tr) > Pima.tr[1:5,] npreg glu bp skin bmi ped age type 1 5 86 68 28 30.2 0.364 24 No 2 7 195 70 33 25.1 0.163 55 Yes 3 5

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

Hello, When I run R CMD build --binary pkgname I get * checking for file 'pkgname/DESCRIPTION' ... OK * preparing 'pkgname': * checking DESCRIPTION meta-information ... OK * cleaning src * removing junk files * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building binary distribution * installing *source* package

Dear R experts. I might be missing something obvious. I have been trying to fix this problem for some weeks. Please help. #data ped <- c(rep(1, 4), rep(2, 3), rep(3, 3)) y <- rnorm(10, 8, 2) # variable set 1 M1a <- sample (c(1, 2,3), 10, replace= T) M1b <- sample (c(1, 2,3), 10, replace= T) M1aP1 <- sample (c(1, 2,3), 10, replace= T) M1bP2 <- sample (c(1, 2,3), 10, replace= T)

Hello! I downloaded a package "multtest" (from bioconductor.org) in R, and installed it by 'R CMD <package>' (after unzipping and taring). The problem is when I say 'library(multtest)' in R, the following error is generated: Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library

Hello, I would like to get the scales of y-axes dependent only on the data points in a particular panel. Have attached a test example below. When using 'relation="free"', it does not make the scales 'free', however when using 'relation="sliced"', I get a warning "Explicitly specified limits ignored in: limitsFromLimitlist(have.lim = have.ylim, lim

Dear all For my research, I am learning classification now. I was trying some example about classification tree pakages, such as tree and rpart, for instance, in Pima.te dataset have 8 variables (include class=type): library(rpart) library(datasets) pima.rpart <- rpart(type ~ npreg+glu+bp+skin+bmi+ped+age,data=Pima.te, method='class') plot(pima.rpart, uniform=TRUE) text(pima.rpart)

Hi, I am a graduate student at Oregon State University pursuing my Masters degree in Computer Science. I am interested in conducting research on the bug reports in many open source projects. I would like to study how the projects manage their bug reports and identifying how Bugzilla and similar bug repository systems could be improved to facilitate this process. I have a bunch of Perl scripts

I note that "current implementations of R use 32-bit integers for integer vectors," but I am working with large arrays that contain integers from 0 to 3, so they could be stored as unsigned 8-bit integers. Can R do this? (FYI -- This is for storing minor-allele counts for genetic studies. There are 0, 1 or 2 minor alleles and 3 would represent missing.) It is theoretically possible

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

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