similar to: Running BayesFst in R

Hi, For the last few days I have tried utilise your package "pegas" in order to obtain some values for indices like the nuclear diversity and tajimas d value. I have modified my dataset (a text file containing dna sequences) in order to be able to read it in with the tools provided by pegas. Here, I have oriented myself on the description provided by the help-page in read.loci().

#Hello, #I have a question about obtaining results from a loop I have written. #Below is a sample of individual genotypes from a genetic question I am working on called "P.genotype.sample ". P.genotype.sample<-matrix(10,10,10) P.genotype.sample[,1]<-c(2,2,1,5,1,1,5,6,1,3) P.genotype.sample[,2]<-c(6,3,3,6,8,1,6,7,2,3) P.genotype.sample[,3]<-c(2,2,2,3,3,2,2,2,3,3)

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("^,", "",

Hi all - I am NEW to R and NEW to any type of programming. I am making heatmaps using the heatmap.2 function within gplots package. At present, when the heatmap is plotted it uses the row identifiers as 1,2,3,4...etc. However, I much rather use my own labels. I was told my another well-versed R programmer to use the follow script: x<-as.matrix(test1[,-1]) ## skip column 1 rownames(x)<-

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.

I am about one step away from heaven on earth. I think only one step! I am using dgc.genetics to run a TDT test on thousands of genetic loci. I have learnt (through the help of others on this mailing list) to send the complex output to useful data frames which in turn allow me to look at the big picture and screen the thousands of loci. Resultdt<-lapply(PGWide[,240:290], tdt) the above

Rers, I have been using the function 'by' in such a manner: by(LogMetric, list(Loci.Number=Loci.Number, Code.Flag=Code.Flag), plot) with par(mfrow=c(5,3)) to produce a single R Graphics: Device with 14 different plots on it as described above in my 'by' statement. Thank you for helping me thus far. A similar command using 'tapply' can be written as well. My

Hi, These are two problems I've never seen when I used xtable() before... R 1.9.1 for Windows XP, xtable version 1.2-3: > final.df Loci Chr Marker Position P.values Deviance DF 1 Idd5 1 D1Mit181 42.6 0.0011 103.21 78 2 Idd6/19/20 6 D6Mit374 66.7 0.0014 104.29 78 3 Idd13 2 D2Mit490 64.5 0.0025 97.83 78 4

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, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency.

# Hello, # I have a list with 6 categories and with different numbers of rows. # I would like to change each of them into a unique data frame in order to match # values with other data frames and perform some calculations. # Or I could make each category or list element have the same number of rows and create one large data.frame. # below is a creation of a sample list # I apologize for the

Dear all, I am running qtl mapping. I have 75 RI lines with some residual heterogeneous loci. The loci are code A, B or H(heterogeneous). Questions: 1) R/qtl determine the data is F2 intercross. 2) Warning message about strange genotype pattern > library(qtl) > dat=read.cross("csv", file="rqtl_trt.csv") --Read the following data: 75 individuals

Dear R-help We have a regression problem which could be solved elegantly if we could figure out how to get the R residuals() function to accept missing dependent variables. We have ~20000 gene-expression vectors y, each being measured on the same set of individuals, but each having a small random number of missing values. For each expression vector we wish to search across the genome

Dear colleagues, I face a problem doing haplotype analyses with haplostats: when I use the haplo.em function, the programme gives an error message because of 'recursive default argument reference.' I am not able to figure out what this means. Could you perhaps help me? The full output is the following: > library(haplo.stats) >

Dear R helpers, I am trying to test for linkage disequilibrium (LD) in R between all pairs of loci. Importantly, my loci are microsatellites and have up to 30 alleles per locus. Do you know of any R packages that can either (1) calculate measures of LD directly or (2) test for the presence of LD within a statistical framework? Every package I have run across seems to be only able to handle

Hi everyone, I'm the developer of the Loci programming language ( http://loci-lang.org ), for which the compiler is a front-end for LLVM. I would like to say that LLVM has been extremely useful for the development of the compiler and so thank you everyone for building this amazing system. ---- Virtual Method Calls ---- While most aspects of the language map well onto LLVM IR, it seems

I?m tryng to use the SPDEP package in my research in the field of population genetics. My data set has the following format: - x and y : coordinates, - Z: allelic frequency in each loci (in a total of 8 locis) - this variable can assume the values 0 ; 0.5 or 1. The objective is to verify if there is a possible spatial autocorrelation structure of the allelic frequency in a population of

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

Hello all, It''s my first letter on this list, and, my English is not very well. Please take me indulgence for grammar/syntax and over erorrs :)) I have trouble for acl''s of ip range. But, acl for one host (with ip adress) work fine. Please help me for make work acl/find erorr in acl. Becouse I''m new shorewall user, I maked test configuration on Virtual Mashine

R-users, I'm seeking any suggestions on optimizing some code for speed. Here's the setup: the code below is part of a larger chunk that is calculating Fst values across loci and alleles. This chunk is designed to calculate the proportion ('p.a') of an allele ('a') at a locus in each population ('p') and the proportion of individuals heterozygous for that