similar to: Re; Getting SNPS from PLINK to R

snpMatrix package is quite nice (read.plink())

Hi All, does anyone know how to import binary .bed files generated by Plink (http://pngu.mgh.harvard.edu/~purcell/plink/ ) into R? the Plink FAQ explains how to conver other types of files, not the .bed. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax

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, ? I am very new to R. So, pardon my dumb question. I was trying to write my own function to run a different model (perform an ordered logistic regression) using the example in website http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml But R returns a error `R Error in eval(expr, envir, enclos) : object 's' not found' when I run it. What am I doing wrong here? Here's

Hello, I am having really hard time finding a good article about simulating genotypes of cases and controls at a disease locus using R. if you guys can point me or guide me where i can find more information, it will be helpful. thanks, Claire -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17065607.html Sent from the R help mailing list archive at

Hi, Following my earlier posts about having problems performing a PCA, I have worked out what the problem is. The problem lies within the PLINK to gds conversion. It seems as though the SNPs are imported as "samples" and in turn, the samples are recognised as SNPs: >snpsgdsSummary("chr2L") Some values of snp.position are invalid (should be > 0)! Some values of

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

Hi all, I have the following code: set.seed(1) x1 <- matrix(sample(1:12), ncol=3) x2 <- matrix(sample(1:12), ncol=3) x3 <- matrix(sample(1:12), ncol=3) X <- list(x1,x2,x3) tt <- matrix(round(runif(5*4),2), ncol=4) Is there a way I can construct a new list where newlist[[i]] = tt[i,] %*% X[[i]] without using a for loop? Each element of newlist will be 3 x 1 vector. Thanks -- Tina

I have a list 'ans' from the following code: tt <- rnorm(50) rr <- rnorm(50) ans <- lm(rr~tt) ans[1] is "$coefficients", ans[2] is "$residuals", ans[3] is "$effects", ... and so on up to ans[12]. Is there an easy way to display just these names and not the data they contain? I thought I saw my advisor type "ans$" and they were displayed,

Hello all, I am interested in simulating 10,000 2 x 3 tables for SNPs data with the Hardy Weinberg formulation. Is there a quick way to do this? I am assuming that the minor allelle frequency is uniform in (0.05, 0.25). -- Thanks, Jim. [[alternative HTML version deleted]]

Hello, I've already tried asking at the cwrRsync forums with no luck yet, so I thought I would try my luck here. According to the rsync man pages, with the -e option you can use other remote shells, and I had thought plink was one of them, but I could be wrong. I can't seem to find any information anywhere about the proper syntax. What I've been trying, are all kinds of combination

Dear All, Does anybody have experience with R package pbatR (http://cran.r-project.org/web/packages/pbatR/index.html)? I am trying to use it to analyze the family-based case-control data, but the package totally doesn?t work on my computer. I contacted the authors of the package, but I haven?t heard anything from them. Following the package manual, I tried the simple example as below:

Hello, I have indicators for the present of absent of a snps in columns and the categorey (case control column). I would like to extract ONLY the tables and the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when one of the allelle is missing. The data look like the matrix snpmat below: so the first snp should give me the following table: (aa=0, Aa=1 and AA=2) aa

Dear R list, I have the following data: set.seed(1) n <- 5 # number of subjects tt <- 3 # number of repeated observation per subject numco <- 2 # number of covariates x <- matrix(round(rnorm(n*numco),2), ncol=numco) # the actual covariates x > x [,1] [,2] [1,] -0.63 -0.82 [2,] 0.18 0.49 [3,] -0.84 0.74 [4,] 1.60 0.58 [5,] 0.33 -0.31 I need to form a matrix

Just a couple of small bug-lets/stuffs in Sweave: - It stripes off the two lines starting with @ (this is a verbatim section showing plink's start-up message): ======================================= @----------------------------------------------------------@ | PLINK! | v0.99p | 17/Dec/2006 | |----------------------------------------------------------| | (C)

Dear Mme/Mr. Hope you are doing well. I am doing some genetic analysis using The R software and I have difficulties to find how I can perform an Interaction/epistasis analysis using 3 or more SNPs (=markers) ? (In the instructive manual, there is only an interaction/epistasis analysis with 2 markers). In addition can you please inform me how I can perform Haplotype analysis and if there is an

CRAN (and crantastic) updates this week New packages ------------ Updated packages ---------------- New reviews ----------- This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: cranatic at gmail.com.

The first version of the package plink has been uploaded to CRAN. plink is a package for conducting unidimensional IRT scaling and chain linking for multiple groups for single-format or mixed-format common items. The package supports eight IRT models and four calibration methods. Dichotomous Models: 1PL, 2PL, 3PL Polytomous Models: -Graded response model -Partial credit model -Generalized

The first version of the package plink has been uploaded to CRAN. plink is a package for conducting unidimensional IRT scaling and chain linking for multiple groups for single-format or mixed-format common items. The package supports eight IRT models and four calibration methods. Dichotomous Models: 1PL, 2PL, 3PL Polytomous Models: -Graded response model -Partial credit model -Generalized

Recently our Unix Administrator installed Samba v.2.07. It was configured to attach to our NT domain. When this occurred we started to experience problems with user authentication's to the domain and it appeared that the "Samba" server had become the master browser. Have you seen this problem occur at other sites? If so, what is the work around? We have been using Samba v2.06