similar to: SNPRelate: Plink conversion

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]]

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

Dear, I am using the R package SNPRelate but I found an error when I run the following command. Do you know what might be the problem? Thanks in advance. > vcf.fn <- system.file("extdata","str.vcf",package="SNPRelate") > snpgdsVCF2GDS(vcf.fn,"test.gds") Start snpgdsVCF2GDS ... Extracting bi-allelic and polymorhpic SNPs.

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

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, I am using the R package SNPRelate but I found an error when I run the following command. Do you know what might be the problem? Thanks in advance. > vcf.fn <- system.file("extdata", "sequence.vcf", package="SNPRelate") > snpgdsVCF2GDS(vcf.fn, "test.gds") Start snpgdsVCF2GDS ... Open

If I run an analysis which generates statistical tests on many SNPs I would naturally want to get more details on the most significant SNPs. Directly from within R one can get the information by loading RSNPer (from Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately, the command cannot handle a vector and therefore only wants to do one at a time. I tried the lapply and

I have a solution (actually a few) to this problem, but none are computationally efficient enough to be useful. I'm hoping someone can enlighten me to a better solution. I have data frame of chromosome/position pairs (along with other data for the location). For each pair I need to determine if it is with in a given data frame of ranges. I need to keep only the pairs that are within any 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

Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matrix with the column means already substracted followed by a

Hi, The program below work very well. (snps = c('rs621782_G', 'rs8087639_G', 'rs8094221_T', 'rs7227515_A', 'rs537202_C')) Selec = todos[ , colnames(todos) %in% snps] head(Selec) But, I have a data set with 1.000 columns and I need extract 70 to use (like snps in command above). This 70 snps are in a file. So I create a file to extract them with

My name is Gert Jensen and I am a newbe to Samba. I have tried installing it a few time and have run into the same problem no matter how I try to get the management module to load. Can someone on the list give me instructions or send me to a site where there are explicit instructions on how to set up SWAP with the latest version of Sambe and Red Hat 7.3. When I try to access

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.

Dear R-devel, I am writing for help on how I should include parallel sets of data in my package. Brief summary: I am new to using data within packages. I want a user to be able to specify one of two alternative versions of within-package datasets to use, and I want to load just that one. I have a solution that works, but it doesn't seem as simple as it should be from a user's

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

An updated version of the package plink has been uploaded to CRAN. This is a major revision that now includes multidimensional models and methods. plink is a package for conducting unidimensional and multidimensional IRT-based test linking using separate calibration methods for multiple groups for single-format or mixed-format common items. The package supports sixteen IRT models and eleven

An updated version of the package plink has been uploaded to CRAN. This is a major revision that now includes multidimensional models and methods. plink is a package for conducting unidimensional and multidimensional IRT-based test linking using separate calibration methods for multiple groups for single-format or mixed-format common items. The package supports sixteen IRT models and eleven

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in

Dear useRs, First off, sorry about the long post. Figured it's better to give context to get good answers (I hope!). Some time ago I wrote an R function that will get all pairwise interactions of variables in a data frame. This worked fine at the time, but now a colleague would like me to do this with a much larger dataset. They don't know how many variables they are going to have in the