similar to: permutation and reshuffling

Dear R helpers I have a table and i need to make new table table1: sire snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10 snp11 snp12 snp13 snp14 snp15 8877 -1 -1 -1 -1 0 0 -1 -1 -1 0 1 1 1 -1 -1 7765 1 1 1 0 0 0 -1 1 1 1 0 0 0 1 0 8766 1 1 -1 0 -1 -1 0 -1 0 -1 -1 -1 0 1 0 6756 0 1 0 -1 1 -1 -1 0 0 0 0 -1 0 1 1 5644 -1 0 1 -1 0 0 0 0 -1 -1 0 0 0 0 1 I have table2 sire

Hello all, I hope some of you can come to my rescue, yet again. I have two genetic datasets, and I want one of the datasets to have only the columns that are in common with the other dataset. Here is a toy example (my real datasets have hundreds of columns): Dataset 1: Individual SNP1 SNP2 SNP3 SNP4 SNP5 1 A G T C A 2 T C A G T 3 A C T

Hi R-help folks, I have been doing some single SNP association work using snpMatrix. This works well, but produces a lot of false positives, because of population structure in my data. I would like to correct the p-values (which snpMatrix gives me) for population structure, possibly using principle component analysis (PCA). My data is complicated, so here's a simple example of what

Hi ihave one table that look like SNP1 SNP2 SNP3 SNP4 SNP5 SIRE1 1 -1 -1 1 -1 SIRE2 1 -1 1 1 1 SIRE3 -1 -1 1 1 0 SIRE4 -1 1 1 0 1 SIRE5 -1 1 -1 -1 1 SIRE6 0 0 0 1 -1 SIRE7 -1 0 -1 1 1 SIRE8 1 -1 NA 0 NA SIRE9 -1 1 1 -1 -1 SIRE10 1 1 1 1 1 table 2 only one line SNP1 SNP2 SNP3 SNP4 SNP5 SIRE100 -1 -1 1

Hi ihave one table that look like SNP1 SNP2 SNP3 SNP4 SNP5 SIRE1 1 -1 -1 1 -1 SIRE2 1 -1 1 1 1 SIRE3 -1 -1 1 1 0 SIRE4 -1 1 1 0 1 SIRE5 -1 1 -1 -1 1 SIRE6 0 0 0 1 -1 SIRE7 -1 0 -1 1 1 SIRE8 1 -1 NA 0 NA SIRE9 -1 1 1 -1 -1 SIRE10 1 1 1 1 1 table 2 only one line SNP1 SNP2 SNP3 SNP4 SNP5 SIRE100 -1 -1 1 1 -1 I need to male

Hello I have two data frames, SNP4 and SNP1: > head(SNP4) Animal Marker Y 3213 194073197 P1001 0.021088 1295 194073197 P1002 0.021088 915 194073197 P1004 0.021088 2833 194073197 P1005 0.021088 1487 194073197 P1006 0.021088 1885 194073197 P1007 0.021088 > head(SNP1) Animal Marker x 3213 194073197 P1001 2 1295 194073197 P1002 1 915 194073197

I'm new to R (previously used SAS primarily) and I have a genetics data frame consisting of genotypes for each of 300+ subjects (ID1, ID2, ID3, ...) at 3000+ genetic locations (SNP1, SNP2, SNP3...). A small subset of the data is shown below: SNP_ID SNP1 SNP2 SNP3 SNP4 Maj_Allele C G C A Min_Allele T A T G ID1 CC GG CT AA ID2 CC GG CC AA ID3 CC GG nc AA

In preparation for 4.00 product release, I have implemented the following changes: a) EXTLINUX is now finally removed as a separate derivative. SYSLINUX and EXTLINUX are fully merged as a single entity. The program extlinux(8) remains as an online nstaller for the SYSLINUX bootloader (ldlinux.sys), since the syslinux program (on Unix) is an offline installer. -> These may get

Hi, I've got a quite tricky question. I have a txt file, named 'temp.txt', as the following: snp1 snp2 snp3 AA 00 00 GG GG 00 00 AA 00 I want to read the file into R. 1) when I use 'read.table' without 'header=T' option, > temp <- read.table('temp.txt') # I got > temp V1

Hi Readers, I have a question. I have a large dataset and want to throw away columns that have the same value in the column itself and I want to know which column this was. For example > x<-data.frame(id=c(1,2,3), snp1=c("A","G", "G"),snp2=c("G","G","G"),snp3=c("G","G","A"))

Hi, I have a large dataset on which I would like to do the following: x<-data.frame(id=c(1,2,3), snp1=c("AA","GG", "AG"),snp2=c("GG","AG","GG"),snp3=c("GG","AG","AA")) > x id snp1 snp2 snp3 1 1 AA GG GG 2 2 GG AG AG 3 3 AG GG AA And then

Hi, I have a question about the data handling. I have a dataset as following: ID snp1 snp2 snp3 1001 0/0 1/1 1/1 1002 2/2 3/3 1/1 1003 4/4 3/3 2/2 I want to convert the dataset to the following format: ID snp1 snp2 snp3 1001 00 AA AA 1002 GG

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

This was exactracted from a 8192x4 texture, with 32x4 tiles. 4 patterns appears, each 8x128 bytes long. these patterns are repeated, and one is always left out. So 123, 234, 134, 124. The repetetive cycle is therefore 4x3x8x128 = 12288 bytes long. I've included the color code ods file, which contains the normal -> actual position. I have no idea how this goes for larger tiles (is the

Hi, My query is regarding permutation test and reshuffling of genotype/phenotype data I have been using the haplo.stats package of R. for haplotype analysis and I would like to perform an analysis which I'm requesting your advice. I have a data set of individuals genotyped for 12 SNP and a dichotomous phenotype. At first, I have tested each of those SNP independently in order to bypass

I would like to randomly shuffle a distance object, such as the one created by ade4{dist.binary} below. My first attempt, using sample(jc.dist) creates a shuffled vector, losing the lower triangular structure of the distance object. How can I Ishuffle the lower triangular part of a distance matrix without losing the structure? Thanks. --Dale x1 <- c(rep(0,4),1) x2 <- c(rep(0,2),rep(1,3))

On Mon, May 22, 2023 at 11:03:26PM -0700, Christoph Hellwig wrote: > On Wed, May 17, 2023 at 10:22:41AM +0800, Xuan Zhuo wrote: > > virtuque_add() adds parameter premapped. > > Well, I can see that. But why? Assuming it's intentional, it should say something along the lines of "The parameter is unused for now, and all callers just pass false. It will be used by a

Thu Jul 12 03:42:12 CDT 2012, Verena Beckham verena at codeplay.com : > I would not say it is trivial, having done it myself. > > MCJIT also doesn't support multiple modules, and it does not do JITing > on demand, instead, it does all of it at the same time in the > constructor (unless that is what you call "not lazy"). > So depending on how you've written your

Hi, Need help on data recovery. Suddenly my disk device's geometry has been changed to something that doesnot make any sense. Its a 1.8TB in size and had only one single partition. Now I can see 3 partitions sde1, sde2 and sde2 of sizes 130M, 140GB and 10GB. Is there any way to recover data from these newly created disk devices? Thanks Paras.

Hi Pawel, Some of the issues I have come across (from memory!) are * MCJIT doesn't work on Windows, because it doesn't support COFF. If you want to use it on Windows you have to either target Mach-O (not clear whether that will work in general) or ELF (need to get a patch from Intel to be able to use this). * Make sure you include MCJIT.h and link in MCJIT.lib, otherwise (even if