similar to: Hardy Weinberg Case Control Test in gap R package

Hello all, I am interested in simulating 10,000 2 x 3 tables for SNPs data with the Hardy Weinberg formulation. Is there a quick way to do this? I am assuming that the minor allelle frequency is uniform in (0.05, 0.25). -- Thanks, Jim. [[alternative HTML version deleted]]

I'm trying to use the IAPWS95 package with the tidyverse packages. For some reason, the function is not outputting the correct rho. A minimal example with results is below. I've also included the definition of the DTp function from the IAPWS95 library. ==================================== library(IAPWS95) library(tidyverse) initial <- data.frame(T=c(279,294),p=c(0.46,0.46))

Hello, I am trying to simulate 10 relicates of 100-tables. Each table is a 2 x 3 and 80% pf the tables are true nulls and 20% are non-nulls. The nulls follow the Hardy Weinberg distribution (ratio) 1:2:1. I have the code below but the p-values are not what I am expecting. I want to use the Cochran Armitage trend test to get the p-values. num.reps=10 num.vars=1000 pi0 = 80 num.subjects = 100

Hi Shawn, I don't think it has anything to do with the tidyverse. If you keep simplifying your example you'll get all the way down to > DTp(T=c(279,294),p=c(0.46,0.46)) [1] 1000.12283 --Ista On Wed, May 30, 2018 at 2:14 PM, Shawn Way <SWay at meco.com> wrote: > I'm trying to use the IAPWS95 package with the tidyverse packages. For some reason, the function is not

Dear All, I am trying to calculate the Hardy-Weinberg Equilibrium p-value for 42 SNPs. I am using the function HWE.exact from the package "genetics". In order not to do a lot of coding "by hand", I have a for loop that goes through each column (each column is one SNP) and gives me the p.value for HWE.exact. Unfortunately some SNP have reached fixation and HWE.exact requires a

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]]

I have a 2 x 3 matrix called snp and I want to compute the following probability: choose(sum(snp[,1]), snp[1,1]) * choose(sum(snp[,2]), snp[1,2]) * choose(sum(snp[,3]), snp[1,3])/choose(sum(snp), sum(snp[1,])) but I keep getting Infs and NaNs. Is there a function that can do this in R? -- Thanks, Jim. [[alternative HTML version deleted]]

Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matrix with the column means already substracted followed by a

Hello, I have indicators for the present of absent of a snps in columns and the categorey (case control column). I would like to extract ONLY the tables and the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when one of the allelle is missing. The data look like the matrix snpmat below: so the first snp should give me the following table: (aa=0, Aa=1 and AA=2) aa

I have a column of 1000 datapoints from the normal distribution with mean 2 and variance 4. How can I get a histogram of these observations with 20 bins with each bin having 50 observations? -- Thanks, Jim. [[alternative HTML version deleted]]

Hi, I have a 2 x 10000 matrix of confidence intervals. The first column is the lower and the next column is the upper. I want to cont how many times a number say 12 lies in the interval. Can anyone assist? -- Thanks, Jim. [[alternative HTML version deleted]]

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

Dear all, I want to simulate from the null distribution of the following 2 x 3 table, 2 5 10 4 8 5 I am using a chi-squared test. Anyone has any idea how to do this? -- Thanks, Jim. [[alternative HTML version deleted]]

Is anyone aware of a fast way of doing fisher's exact test for a series of 2 x 2 tables in R? The fisher.test is really slow if n1=1000 and n2 = 1000. -- Thanks, Jim. [[alternative HTML version deleted]]

https://bugs.freedesktop.org/show_bug.cgi?id=32855 Summary: Incorrect image stretching with Render in RepeatPad mode, NV50 Product: xorg Version: git Platform: x86-64 (AMD64) OS/Version: Linux (All) Status: NEW Severity: normal Priority: medium Component: Driver/nouveau

Hello all, I have two columns of numbers. I would like to do the following: (1) Plot both cdfs, F1 and F2 on the same graph. (2) Find smoothed approximations of F1 and F2 lets call them F1hat and F2hat (3) Find values for F1hat when we substitue a value of x in it. (4) Find the corresponding densities of the cdfs. Any ideas? -- Thanks, Jim. [[alternative HTML version deleted]]

Hello everyone, I am trying to estimate the parameter b. I have Y and X1 which I know and they are both random. However, I also have X2 which I don't know and is also random. I want to estimat b from the model: Y = b*X1 + ( 1 - b ) * X2 Can anyone offer some suggestions. The values of Y and X1 are both pvalues so they are constrained in (0,1). -- Thanks, Jim. [[alternative HTML version

Suupose I have y <- rbeta(10000, 2, 5) and I only want to see only the density plot from x = 0 to x = 1 How do I do this? -- Thanks, Jim. [[alternative HTML version deleted]]

I am doing a histogram with 2 superimposed densities. However, the density of one of the graphs is not coming out..its being erased.. Any ideas on how to fix this problem? -- Thanks, Jim. [[alternative HTML version deleted]]