similar to: Pedigree / Identifying Immediate Family of Index Animal

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

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

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

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",

Hello, I am building a R-package for Genetics analysis. The accepted data is in pedigree (.ped) file format. To load the data (say CAMP.ped) from "data" directory, I have a function "CAMP.R", which does the job. The package builds successfully in Linux (.tar.gz) and the data loads successfully by "data(CAMP)". However, when I build the package in WINDOWS, the data

I have an S3 class called "tis" (Time Indexed Series) which may or may not have multiple columns. I have a function "[<-.tis" that I've reproduced below. My question is this: inside of "[<-.tis", how can I distinguish between calls of the form x[i] <- someValue and x[i,] <- someValue ? In either case, nargs() is 3, and looking at the values

I have an S3 class called "tis" (Time Indexed Series) which may or may not have multiple columns. I have a function "[<-.tis" that I've reproduced below. My question is this: inside of "[<-.tis", how can I distinguish between calls of the form x[i] <- someValue and x[i,] <- someValue ? In either case, nargs() is 3, and looking at the values

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 all identifiers appear in the individual column - it is

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

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

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

Hi Bogdan, Messy, and very specific to your problem: df.sample.gene<-read.table( text="Chr Start End Ref Alt Func.refGene Gene.refGene 284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3 448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194 465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910 525 chr2 223777758 223777758 T A

If row numbers can be dispensed with, then tidyr makes this easy with the unnest function: ##### library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union library(purrr)

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

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 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)

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

Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work > summary(founders[,59]) to prove that it is a genotype class > class(founders[,59]) [1] "genotype" "factor" Now when I issue the command: > summary(founders[,59]) I get: Error in attr(retval, "which") <- which :