similar to: predict.gl( ..., type="terms" )

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]]

On Sun, May 31, 2015 at 7:12 AM, The Doctor <doctor at doctor.nl2k.ab.ca> wrote: > So far BSD/OS and opensh 6.9 pre works with ZOC and Tera Term. > > Putty and 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

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: read.table(file, header = FALSE,

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

Hi, Is the 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

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

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

Is it possible to move a server's public and private keys from one host to another? Or perhaps a better way to ask what I really want... is it possible to configure a server on a new host to return the same public key it did on the old host? I'm in the process of migrating our CVS server from a Solaris host to a Linux host (this weekend) and I just realized the hostkey is going to

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

Hi, We are preparing to make the release of OpenSSH 4.8 soon, so we would greatly appreciate testing of snapshot releases in as many environments and on as many operating systems as possible. The highlights of this release are: * Added chroot(2) support for sshd(8), controlled by a new option "ChrootDirectory". Please refer to sshd_config(5) for details, and please use this

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 the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I

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, ? 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

I am trying to model survival data with a Weibull distribution using survreg. Units are clustered two apiece, sometimes receiving the same treatment and sometimes opposing treatment.

I''m a newb to programming. I heard about ruby on rails from some web design friends. I''ve been reading different "Why''s (poigrant) guide to ruby" and Finished Rails for Zombie in code school. I''ve download ruby 1.9.2 for window, but not sure what other software i need to get started. -- You received this message because you are subscribed to the

This is a request for a How-To I need to SSH from my Windows 7 laptop to several Linux machines that are inside a secondary VPN. To explain: I have a network (Call it LAN A), containing a few Windows 2K servers, that is protected by a VPN. That network connects to another one (call it LAN B), that has a few Linux server, over a separate site-to-site VPN. >From outside (here) I have no access

Hi, I have a problem regarding matrix handeling. I am working with a serie of matrixes containing several columns. Now I would like to delete those rows of the matrixes,that in one of the columns contain values less than 50 or greater than 1000. How would this be possible, I have tried to create a simple function for this, but I just don't seem to get it right.Thank you so much for your help,

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

I am a test engineer, testing SSH server implementation of SSH into one of our switches. How can I automate the login and logout of an SSH client from the command line? I have in a script file the following, but I get prompted for the password. How can I automate the password and the exit. ssh2 -l $1 $2 (ssh2 -l <username> <host ip>) Theresa C. Karpowicz Software