search for: gwas

Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of issues: First, I am having a problem reading files (.map, & .ped, size 900Mb, using windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking this problem is likely due to the large size of the files & my version of R is not able...

Hello to the list I'm using a Rscript launched via the linux terminal as the title of this mail explains. The following is the code of the Rscript : myRscript.r -------------------------------- 1 #!/usr/bin/Rscript 2 3 #Read data 4 data=read.table("/home/morisseau/stage/recherche/gwas/data/CFHLC5/CFHLC_format_files_rm_07052010/output/windowstemp.txt") 5 6 data=t(data) 7 phen=read.table("/home/morisseau/stage/recherche/gwas/data/CFHLC/CFHLC_format_files_rm_07052010/input/Admixmap_simphen_simu1_causalsnp61.txt") 8 phen=phen[-1] 9 phen=t(phen) 10 val=c(1,2) 11 for (i...

...in single.snp.association) for population structure? In my real data, population structure is causing a lot of type I errors (false positive SNPs). I have read of some standalone software that does this sort of thing, for example EIGENSTRAT: http://www.biostat.jhsph.edu/~iruczins/teaching/misc/gwas/papers/price2006.pdf But I'd like to stick to R if possible. Any advice/comments welcome.

...multihreaded with OpenMP. I also implemented the possibility to check for user interruption, using the work-around by Simon Urbanek. I just uploaded the package on my R-forge project, so you should be able to get the package from https://r-forge.r-project.org/scm/viewvc.php/pkg/RcppProgress/?root=gwas-bin-tests * The progress bar is displayed using REprintf, so that it works also in the eclipse StatET console, provided that you disable the scroll lock. * You should be able to nicely interrupt the execution by typing CTRL+C in the R console, or by clicking the "cancel current task" in...

...0365313727164e-86858901" > > already gives a rarely seen small p value. I gather I also need a multiple precision exp() and their sum since exp(z^2/2) is also a Bayes Factor so I get log(x_i )/sum_i log(x_i) instead. To this point, I am obliged to clarify, see https://statgen.github.io/gwas-credible-sets/method/locuszoom-credible-sets.pdf. > > I agree many feel geneticists go to far with small p values which I would have difficulty to argue againston the other hand it is also expected to see these in a non-genetic context. For instance the Framingham study was established in 19...

You may want to look into using the log option to qnorm e.g., in round figures: > log(1e-300) [1] -690.7755 > qnorm(-691, log=TRUE) [1] -37.05315 > exp(37^2/2) [1] 1.881797e+297 > exp(-37^2/2) [1] 5.314068e-298 Notice that floating point representation cuts out at 1e+/-308 or so. If you want to go outside that range, you may need explicit manipulation of the log values. qnorm()

...03192917090365313727164e-86858901" already gives a rarely seen small p value. I gather I also need a multiple precision exp() and their sum since exp(z^2/2) is also a Bayes Factor so I get log(x_i )/sum_i log(x_i) instead. To this point, I am obliged to clarify, see https://statgen.github.io/gwas-credible-sets/method/locuszoom-credible-sets.pdf. I agree many feel geneticists go to far with small p values which I would have difficulty to argue againston the other hand it is also expected to see these in a non-genetic context. For instance the Framingham study was established in 1948 just go...

...to test it. In the meantime Petr Savicky contacted saying he was about to release a similar package called rngOpenMP. So I decided to perform some quick benchmarks. The benchmark code is available as a R package "rngBenchmarks" here: https://r-forge.r-project.org/scm/viewvc.php/pkg/?root=gwas-bin-tests but it depends on some unpublished package, like rngOpenMP, and my preliminary package, yet available from the same URL. As a benchmark I implemented a Monte-Carlo computation of PI. I tried to use the exact same computation method, using a template argument for the RNG, and providing wr...

...> > > > already gives a rarely seen small p value. I gather I also need a > multiple precision exp() and their sum since exp(z^2/2) is also a Bayes > Factor so I get log(x_i )/sum_i log(x_i) instead. To this point, I am > obliged to clarify, see > https://statgen.github.io/gwas-credible-sets/method/locuszoom-credible-sets.pdf > . > > > > I agree many feel geneticists go to far with small p values which I > would have difficulty to argue againston the other hand it is also expected > to see these in a non-genetic context. For instance the Framingham st...

...es a rarely seen small p value. I gather I also need a >> multiple precision exp() and their sum since exp(z^2/2) is also a Bayes >> Factor so I get log(x_i )/sum_i log(x_i) instead. To this point, I am >> obliged to clarify, see >> https://statgen.github.io/gwas-credible-sets/method/locuszoom-credible-sets.pdf >> . >> > >> > I agree many feel geneticists go to far with small p values which I >> would have difficulty to argue againston the other hand it is also expected >> to see these in a non-genetic...

...es a rarely seen small p value. I gather I also need a >> multiple precision exp() and their sum since exp(z^2/2) is also a Bayes >> Factor so I get log(x_i )/sum_i log(x_i) instead. To this point, I am >> obliged to clarify, see >> https://statgen.github.io/gwas-credible-sets/method/locuszoom-credible-sets.pdf >> . >> > >> > I agree many feel geneticists go to far with small p values which I >> would have difficulty to argue againston the other hand it is also expected >> to see these in a non-genetic...

CRAN (and crantastic) updates this week New packages ------------ * disclapmix (0.1) Maintainer: Mikkel Meyer Andersen Author(s): Mikkel Meyer Andersen and Poul Svante Eriksen License: GPL-2 http://crantastic.org/packages/disclapmix disclapmix makes inference in a mixture of Discrete Laplace distributions using the EM algorithm. * EstSimPDMP (1.1) Maintainer: Unknown Author(s):

CRAN (and crantastic) updates this week New packages ------------ * allan (1.0) Alan Lee http://crantastic.org/packages/allan Automates Large Linear Analysis Model Fitting * andrews (1.0) Jaroslav Myslivec http://crantastic.org/packages/andrews Andrews curves for visualization of multidimensional data * anesrake (0.3) Josh Pasek http://crantastic.org/packages/anesrake This