search for: ped

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 sometin...

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&qu...

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 WI...

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 77 82 41 35.8 0.156 35 No 4 0 165 76 43 47.9 0.259 26 No 5 0 107 60 25 26.4 0.133 23 No > > dimnames(Pima.tr)[[2]] [1] "npreg" "glu" "bp"...

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....

...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 random example data > > #********************pedigree data***************************** id <- 1:100 dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7, 10), rep(9, 10), rep(11, 10), rep(13, 10), rep(15, 10), rep(17, 10), rep(19, 10), rep(21, 10)) momid <- c(rep(0, 5), rep(2, 5), rep(4, 5), rep(6, 5), rep(8, 10), rep(10, 10)...

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) # variable set 2 M2a <- samp...

...re 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 operations inside function to do this. My question this time is I want to do this seperately for each level of factor (infollowing example it is Ped, thus if there are 20 ped, I want a output with 20 statistics, so that I can work further on them). #data generation ped <- c(1,1,1,1,1, 1,1,1,1,1, 2,2,2,2,2, 2,2,2,2,2)# I have 20 ped fd <- c(1,1,1,1,1, 2,2,2,2,2, 3,3,3,3,3, 4,4,4,4,4) # I have ~100 fd iid <- c(1:20) # number can g...

...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...

I was suggested to install two tar-red and gzip-ped packages that are not part of CRAN or BioConductors yet. I read the R manual about Administration and could only find a good description of how to install packages not canonically included in CRAN repository, on UNIX systems..... I work on Linux/SuSE and Windows ... so I am stuck with such an ins...

...rep(1, 5), rep(3, 5), rep(5, 5), rep(7, 10), rep(9, 10), rep(11, 10), rep(13, 10), rep(15, 10), rep(17, 10), rep(19, 10), rep(21, 10)) momid <- c(rep(0, 5), rep(2, 5), rep(4, 5), rep(6, 5), rep(8, 10), rep(10, 10), rep(12, 10), rep(14, 10), rep(16, 10), rep(18, 10), rep(20, 10), rep(22, 10) ) ped <- data.frame(id, dadid, momid) cfam <- makefamid(ped$id,ped$momid, ped$dadid) kmat <- makekinship(cfam, ped$id, ped$momid, ped$dadid) set.seed(3456) SNPdata <- c(1:1000) dat <- sample(c(-1,0,1), 10000, replace = TRUE) snpmat<- data.frame(matrix(dat, ncol = 100)) names(snpm...

I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? -- Thanks, Jim. [[alternative HTML version deleted]]

...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) summary(pima.rpart) In the result I found only 5 variables: npreg, glu, bmi, ped, and age were showing in the plot. Now, I have 50 variables in my dataset. The result my classification tree very difficult...

...what I understand it is doing what I would like for the father (example below). Can anyone provide me with some information about this tdthap behaviour? And is there any other package that would do this? (Searched for it, couldn't find it) Thank you very much, Tiago Magalh?es example (ped file with pedigrees) 9 100 102 101 1 2 1 1 2 1 2 2 1 2 9 101 0 0 2 1 1 1 2 1 2 2 2 2 9 102 0 0 1 1 2 1 2 1 2 2 1 1 data out: hap.transmit(example) ped id father mother 9 100 102 101 f.tr.1 f.tr.2 f.tr.3 f.tr.4 1 0 2 1 m.tr.1 m.tr...

Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of issues: First, I am having a problem reading files (.map, & .ped, size 900Mb, using windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking this problem is likely due to the large size of the files & my version of R is not able to handle them, since I can read in smaller files. Second, and the more precedent issue, is with the lo...

...ta 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 words one human, one row. If there were multiple loci then the variables would continue to be heaped up on the right. This kind of orientation, shall be referred to as "wide". Given how big my dataset is, it is easier to manage the data in the database in the "long" format. In this format I have a pedigree table and from it, a one to many relationship with the SNP data. The SN...

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)...

...xa.c:142:31: error: 'CREATE_PIXMAP_USAGE_SHARED' undeclared (first use in this function) QA Contact: xorg-team at lists.x.org Severity: normal Classification: Unclassified OS: Linux (All) Reporter: fabio.ped at libero.it Hardware: x86 (IA32) Status: NEW Version: git Component: Driver/nouveau Product: xorg Compiling on Ubuntu 12.04 leads to this error: make[3]: Entering directory `/build/buildd/xserver-xorg-video-nouveau-1.0.6+git1302061522.e8f222~g...

I try to display the grouping variable in coplot. It work, but it's special solution and rather ugly. Any better idea? # Simulate my data frame data(state) x77<-data.frame(state.x77) x77$region<-state.region coplot(Life.Exp ~ Income | region, data=x77, show.given=F, subscripts=T, panel = function(x, y,subscripts, ...) { panel.smooth(x, y, span = 1., ...)

...have a 'gwaa' data, but I need to add some dummy parents, for 'gwaa at phdata', it's easy to add these rows, but for 'gwaa at gtdata', I think I need to create SNP data as '0 0 0 0 0.....' for all the dummy parents first. I am using the function 'convert.snp.ped', so I need a 'pedfile' of this format: #ped id fa mo sex trait snp1.allele1 snp1.allele2 snp2.allele1 snp2.allele2 ...# 1 1 0 0 1 2 0 0 0 0 ... 1 2 0 0 1 0 0 0 0 0 ... 1 3 0 0 2 1 0 0 0 0 ... . . 100 101 0 0 2 1 0 0 0 0 ... If we use the 1M microarray, usually, after QC, there will...