similar to: integer and floating-point storage

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]]

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

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

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

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, ? 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

Dear All, The following code extracts from NCBI very nice output for ONE allele of a SNP (often the allele with the second largest frequency - usually termed the minor allele). It gives an average minor allele frequency from all NCBI sources (which is what I want, except I'd like the addition of data for all the other alleles of one SNP) plus a table of minor allele frequencies from each

Hello R-help community, I have another question about filtering datasets. Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus

Hi all, [this is a bit hard to describe, so if my initial description is confusing, please try running my code below] #WHAT I'M TRYING TO DO I'd appreciate any help in trying to speed up some code. I've written a script that converts a matrix of integers (usually between 1-10,000 - these represent allele names) into two new matrices of normally distributed values (representing

I have a vector of 2,1,0 I want to change to 0,1,2 respectively (the data is allele dosages) I have tried multiple nested if/else statements and looked at the ?if help and cannot work out what is wrong, other people have posted code which is identical and they state works. Any help would be greatly appreciated. > A[1:20] [1] 1 1 0 0 1 0 1 0 1 0 0 0 1 1 0 1 1 1 0 0 > B <-

Hello All, Once again thanks for all of the help to date. I am climbing my R learning curve. I've got a few more questions that I hope I can get some guidance on though. I am not sure whether the etiquette is to break up multiple questions or not but I'll keep them together here for now as it may help put the questions in context despite the fact that the post may get a little long.

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)

I am involved in a study where, as in most of life, men demonstrate themselves to be recalcitrant. So while we have many probands and most of their mothers we only have about 50% of the trios being complete. I have been running tdt and trio.types. It appears as if it is ignoring the duos. Sometimes a duo can be informative. For instance Father ..missing Mother 1/2 Proband 1/1 This duo shows that

I have a vector: alleles.present<-c("D3", "D16", ... ) The alleles present changes given the case I'm dealing with - i.e. either all of the alleles I use for my calculations are present, or some of them. Depending on what alleles are present, I need to make matrices and do calculations on those alleles present and completely disregard any formula or other use of the

Dear R user: I am studying the allele data of two populations. the following is the data: a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 pop1 0.0217 0.0000 0.0109 0.0435 0.0435 0.0000 0.0109 0.0543 0.1739 0.0761 0.1413 0.1522 0.1087 0.0870 0.0435 0.0217 0.0109 pop2 0.0213 0.0213 0.0000 0.0000 0.0000 0.0426 0.1702 0.2128 0.1596 0.1809 0.0957 0.0745 0.0106

Hi people, I have made some progress trying to work out how to solve this problem but I have got a bit stuck - sorry if this turns out to be a simple exercise . . Allelic Differentiation (AD) in genetics measures the number of different alleles between (say) two populations eg: Organisms in Pop 1 have alleles: a, b, c, d, e Organisms in Pop 2 have alleles: b, b, c, d, e Different

I know that there are quite a few packages out that there for cluster analysis. The problem that I am facing is finding a package that will not incorporate all my samples into clusters but just the samples that fit a threshold (that I have not set yet and may need help finding the right level) for genotyping. It should be able to "no call" samples outside the clusters. It also needs to

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

Dear R listers, I have a data file looks like the following: Testing marker: s_1 --------------------------------------------- Allele df(0) -LnLk(0) df(T) -LnLk(T) ChiSq p 3 7995 29320.30 7994 29311.85 16.90 4e-05 (2229/8000 probands) Testing marker: s_2 --------------------------------------------- Allele df(0)

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,