search for: plink

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())

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 +4...

...nd WINSCP are broken. > Could you please elaborate on "broken"? Which version of PuTTY? (I'm not familiar with WinSCP versions but I believe the code is based on PuTTY, so I think if we figure out PuTTY then the same will probably apply to WinSCP). Could you please run sshd and plink in debug mode ("/eg path/to/sshd -ddde -p 2022" and "plink -v -P 2022 yourhost") -- Darren Tucker (dtucker at zip.com.au) GPG key 8FF4FA69 / D9A3 86E9 7EEE AF4B B2D4 37C9 C982 80C7 8FF4 FA69 Good judgement comes with experience. Unfortunately, the experience usually comes...

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 close to the following: rsync.exe -e "plink.exe -l username -pw password" --stats --compress --recursive --archive --d...

Hello All, This works, results <- read.table("plink.txt",T) while this doesn't. results <- read.table("plink.txt") Make sure your data frame contains columns CHR, BP, and P What does adding the "T" in read.table do? Which argument does this correspond to? I tried searching for it but didn't find the answer in:...

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: -...

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: -...

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 it...

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 it...

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 snp.chromosome are invalid (should be finite and &g...

...file /usr/local/etc/ssh/old_ssh_host_rsa_key debug1: PEM_read_PrivateKey failed debug1: read PEM private key done: type <unknown> Could not load host key: /usr/local/etc/ssh/old_ssh_host_rsa_key The biggest problem is with all our Windows users. Since they only use SSH (really plink) for CVS access, the CVS command fails if plink detects the hostkey has changed. This is really because the cvs command will fail if it gets ANY response it doesn't understand. Many (most) of our Windows users use various GUI CVS clients that often hide any output plink might display, but...

...e rsync-minimalist still supported for windows? I am using Windows XP Home. I am testing, to get a solution for a client. The minimalist looked very nice--a cygwin.dll and an rsync and an ssh.exe. However, I can connect with ssh, but not with rsync over ssh using these files. I have also tried plink from putty with this rsync. I gather from a lot of the messages that the consenus is to install Cygwin. However, I used a long time ago and it was nasty. Visiting their site and perusing the docs confirms it is still pretty complicated for the task. I don't want the registry modified, I wa...

..., 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 to store such data with four integers per byte. This is what PLINK (GPL license) does in its binary (.bed) pedigree format: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped That might be too much to hope for. ;-) I think that the R system uses double-precision floating point numbers by default. When I impute minor-allele counts, I get posterior exp...

.... I''ve looked into > >>net::ssh for ruby but I > >>run into some threading issues, I haven''t been > able > >>to decipher exactly > >>where these issues occur for a number of reasons. > I > >>have turned to > >>using plink.exe (comes with putty.exe) I can > create > >>a secure link with > >>a linux box running ssh and squid. I then point > my > >>browser at the port > >>plink is listening on and voila, I have a secure > >>tunnel to a proxy. > >> > &gt...

...allows callers of ssh(1) to better detect and deal with stuck servers that accept a TCP connection but don't progress the protocol, and also makes ConnectTimeout useful for connections via a ProxyCommand. * Many new regression tests, including interop tests against PuTTY's plink. * Support BSM auditing on Mac OS X This release also contains many bugfixes. Please refer to the tracking bug https://bugzilla.mindrot.org/show_bug.cgi?id=1353 for a partial list. The ChangeLog file in the portable OpenSSH tarballs contains a full list. Please fetch and test the release that i...

...50,80,10), Bo=c(40,90) ) + + ns( Cx, knots=seq(1880,1940,20), Bo=c(1840,1960) ) + + ns( Px, knots=seq(1960,1980,10), Bo=c(1940,2000) ) + + offset( log( Y ) ), + family=poisson ) > pterm <- predict( apc, type="terms" ) > plink <- predict( apc, type="link" ) > ( apply( pterm, 1, sum ) + log( Y ) - plink )[1:10] 1 2 3 4 5 6 7 8 9 10 6.85047 6.85047 6.85047 6.85047 6.85047 6.85047 6.85047 6.85047 6.85047 6.85047 > coef( apc )[1] (Intercept) -13....

...ing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christophe at svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe

Is there some way to do this? I've got the current putty (actually, putty-cac), pageant, and plink in my user's Downlods directory - neither he nor I have admin authority on his laptop, and Desktop support's teleworking today - but I can't seem to find a way to configure xming to look there for putty. Or is it start putty, *then* start xming? mark

Hi all, I'm running HeidiSQL in wine, and it can do ssh tunnels, but only using plink.exe. So can I create a fake plink, that is actually a linux program, that will grab the command line arguments Heidi sends and do my own ssh -L with it? I tried just calling a bash script plink.exe but wine didn't like that. Any ideas? Thanks!