similar to: Rsync with 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 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, 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

On Thursday, 20 September 2018 10:50:14 CEST Richard W.M. Jones wrote: > +# Choose a random port number in range [50000,59999] > +imageio_port = random.randint(50000,60000) > + > [...] > + > +def server(): > + server_address = ("", imageio_port) > + httpd = HTTPServer(server_address, RequestHandler) > + httpd.serve_forever() The random port can be

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

Hey All, After RTM, web page and searching the archives, I felt it worth a shot at mailing the list with my query. I am looking at using rsync and various third party GUI's (rsyncX, nasbackup) to backup our departmental desktops to our nice new multi-terabyte fileserver. When we run rsync in daemon mode, it of course runs as nobody:nogroup and I am aware of being able to set that to any

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

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,

Hi, I have written a C code which would let me connect to the Asterisk Manager Interface. The code compiles successfully but on running the code I get unauthorized login shown in the Asterisk command line console. Here is my C code: #include<stdio.h> #include<netdb.h> #include<unistd.h> #include<string.h> #include<arpa/inet.h> #include<sys/types.h>

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

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

When I do: > apc <- glm( D ~ ns( Ax, knots=seq(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,

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

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

On Thu, Sep 20, 2018 at 11:51 AM Richard W.M. Jones <rjones@redhat.com> wrote: > Previously this output method was almost completely untested. > > This commit adds a fake ovirtsdk4 module so we can test the > -o rhv-upload method fairly completely without needing an actual > oVirt instance around. > --- > v2v/Makefile.am | 4 + >