similar to: Genotypes are not all the same

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

Sequenom has an odd format of calling a SNP genotype gg [1] "C" "GA" "A" "C" "C" "AG" "C" "C" "T" "G" homozygous A is called A and heterozygous is called AT The genetics package cannot handle the fact that some genotypes are declared with 2 letter while other are declared with only 1.

Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work > summary(founders[,59]) to prove that it is a genotype class > class(founders[,59]) [1] "genotype" "factor" Now when I issue the command: > summary(founders[,59]) I get: Error in attr(retval, "which") <- which :

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

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

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

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

Hi All, I have a problem trying to get a set of columns recognised as a list and can't work out how to do it despite trawling through the mailing list archives, and docs. A short example... to.convert <- NULL n <- 6 for(x in 1:n){ to.convert <- paste(to.convert, paste((2 * x) -1, (2 * x), sep=":"), sep=",") } to.convert <- gsub("^,", "",

I evaluated the Bayes factor in the k=2 allele case with a "triangular" prior under the null as in the example in the help file: HWETriangBF2(nvec=c(88,10,2)) [1] 0.4580336 When I swap the n11 entry and n22 entry of nvec, I received totally different Bayes factor: > > HWETriangBF2(nvec=c(2,10,88)) [1] 5.710153 > In my understanding, defining the genotype frequency as

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.

Hi everyone, I'm using the function 'HWE.exact' of 'genetics' package to compute p-values of the HWE test. My data set consists of ~600 subjects (cases and controls) typed at ~ 10K SNP markers; the test is applied separately to cases and controls. The genotypes are stored in a list of 'genotype' objects, all.geno, and p-values are calculated inside the loop over all

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

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

Hi, I am conducting an association analysis of genotype and a phenotype such as cholesterol level as an outcome and the genotype as a regressor using multiple linear regression. There are 3 possibilities for the genotype AA, AG, GG. There are 5 people with the AA genotype, 100 with the AG genotype and 900 with the GG genotype. I coded GG genotype as 1, AG as 2 and AA as 3 and the p-value for the

Hi, Does anybody know how to obtain the imputed SNP genotype probabilities from the snpStats package? I am interested in using an imputation method implemented in R to be further used in a simulation study context. I have found the snpStats package that seems to contain suitable functions to do so. As far as I could find out from the package vignette examples and its help, it gives the

Hi, I have a genotype data for both case and controls and would like to calculate the HW p-value. However, since the number of one genotype is 0, I got wired result. Would someone help me to figure it out? Or confirm it's right? Thanks a lot. ============ > library( "genetics" ) NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced

Dear R-experts, My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis. PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R. How do I open a text-file, line by line,

Dear all, I have data.frame object in R. I want to export it in tab-delimited file with several lines of header initiated with comment sign (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ################################################################## The lines I want to write in the header lines look like, with words

Hi, I am new to R. and even though I've made my code to run and do what it needs to . It is taking forever and I can't use it like this. I was wondering if you could help me find ways to fix the code to run faster. Here are my codes.. the data set is a bunch of 0s and 1s in a data.frame. What I am doing is this. I pick a column and make up a new column Y with values associated with that