search for: locus

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here: http://...

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which is the name or id of the locus. I am able to get the tdt to run by each locus. >tdt(Genotype.914186, PGWide, famid, pid, fatid, motid, sex, affected ) Clearly I cann...

Hello, I have a data-frame in which one-column is a factor: > str(data); `data.frame': 194 obs. of 8 variables: $ Type : Factor w/ 3 levels "Nuclear-Rec..",..: 1 2 2 2 2 2 2 2 2 2 ... $ Locus : num 0.000571 0.004000 0.001429 0.004857 0.007429 ... And I'd like to make a boxplot of the data$Locus values, where each level of the factor gets its own box-and-whiskers plot. I'm weak in R, but I thought there might be some shortcut to automating this instead of just creating...

Hi all, I've been looking in R for an EM algorithm adjusted for multiple-locus haplotypes frequencies, but failed in 100%. Has anyone heard of anything of this kind in R? Thanks in advance, Marcin

#If I have two lists as follows a1<- array(1:6, dim=c(2,3)) a2<- array(7:12, dim=c(2,3)) l1<- list(a1,a2) a3<- array(1:4, dim=c(2,2)) a4<- array(5:8, dim=c(2,2)) l2<- list(a3,a4) #how can I create a new list with the mean across all arrays within the list, so all components are included? As an example for [[1]]; cbind((l1[[1]][,1]+l2[[1]][,1])/2,

...cmat[Gmax,Gtru] = cmat[Gmax,Gtru] + 1 } } ## APPROACH 2: Nested lapply #### # This routine finds the geno w/ highest prob from the erg.avgs. # and compares it to the true geno. Result is tallied by # incrementing the appropriate index of the confusion matrix add2cmat <- function(ind,locus) { Gmax = which.max(c( data[[paste("G_hat_0_",ind,sep="")]][locus], data[[paste("G_hat_1_",ind,sep="")]][locus], data[[paste("G_hat_2_",ind,sep="")]][locus] )) Gtru = data[[paste("G_",ind,sep="")]][locu...

..., 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0), nrow = 5, byrow = T) rland <- new.local.demo(rland,SZ,RZ,M) rland <- new.epoch.island(rland,0,c(0,0,0,0,0),c(0,0,0,0,0),0,c(0,0,0,0,0),c(0,0,0,0,0), 0,c(0,0,0,0,0),c(0,0,0,0,0), carry = rep(carrycap,habitats)) rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, numalleles = 1, mutationrate = 0.001) rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, numalleles = 1, mutationrate = 0.001) rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, numalleles = 1, mutationrate = 0.00...

...w = T) >> >> rland <- new.local.demo(rland,SZ,RZ,M) >> >> rland <- >> new.epoch.island(rland,0,c(0,0,0,0,0),c(0,0,0,0,0),0,c(0,0,0,0,0),c(0,0,0, >> 0,0), >> 0,c(0,0,0,0,0),c(0,0,0,0,0), carry = rep(carrycap,habitats)) >> >> rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, >> numalleles = 1, mutationrate = 0.001) >> rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, >> numalleles = 1, mutationrate = 0.001) >> rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, &g...

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidea...

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, rep...

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, rep...

...lp 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 (e.g., "Locus1" or "Locus2", ... or "Locus6"), the individuals have either one allele (from the set of A,T,C,G) or one other allele (from the set of A,T,C, G). For example, at Locus1 in...

On Fri, 16 Jan 2009, r-help-request at r-project.org wrote: > Date: Thu, 15 Jan 2009 13:29:03 +0100 > From: Pablo G Goicoechea <pgoikoetxea at neiker.net> > Subject: Re: [R] How to create a chromosome location map by locus ID > To: Sake <tlep.nav.ekas at hccnet.nl> > Cc: r-help at r-project.org > Message-ID: <496F2C0F.3040304 at neiker.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Sake: > If you do not find an answer within the list, MapChart will probably...

...155 307 312 I tried to prepare the cast() but didn't quite figure out how to achieve this. I tried to first merge with the following: genMelt <- melt(geno, id = c(1:2, 5:6)) then I created a column: genMelt$Locus <- substring(as.character(genMelt$Panel),5, 6) genMelt$Locus <- paste(genMelt$Locus, genMelt$variable, sep = "_") So I get a column in the appropriate format. But when I cast : mycast <- cast(genMelt,sample_id~Locus) I get just the frequencies of...

...rixS,matrixM) matrixRR <- matrix( c(rep(0,6*6)), ncol=6,nrow=6,byrow=TRUE ) matrixSS <- matrix( c(rep(0,6*6)), ncol=6,nrow=6,byrow=TRUE ) matrixMM <- matrix( c(rep(0,6*6)), ncol=6,nrow=6,byrow=TRUE ) penguinland <- new.epoch(penguinland,matrixRR,matrixSS,matrixMM) penguinland <- new.locus(penguinland) penguinland <- new.individuals(penguinland, c(6, 4, 4, 3, 2, 5)) ## i get error here when simulate.landscape() executed... #+ #+ ERROR MSG: #+ #+ Error in "[<-"(`*tmp*`, slice[l, ], slice[l, ], value = c(0.200000002980232, : #+ number of items to replace is no...

I'm sorry everyone for the inconvenience of spamming the R-help... Here's the complete post: Hi everyone, > > Since it's quite a while that I used the reshape package, I now feel kind > of rusty. > > I have a data.frame like this: > > > > id Sample.Name Marker Allele.1 > Allele.2 sample_id species

Dear R users, I am sorry to disturb you! But I really need your help for the usage of sigPathwy. Actually, I want a sliding window analysis for possible chromosome expression pattern mining. My research microorganism is a plant pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really want to see whether among the continual 10, 20, 30, or 40 locus has some expression pattern that different from rest genes. Because I know sigPathway (R package, pathway analysis with microarray data) can d...

...R all the maximum values together. I would like to graph the lines without having manually do one at a time. I have included a sample of my data below. I have attached a PDF file of what I would like the final product to look like. Any suggestions would be greatly appreciated!! cheers, Jolene locus min max K9/10* 70 72 Pcc40 80 81 2F9 84 100 4E8/Pca12 96 108 Pau6 99 103 Pau20 100 113 Pau9 103 129 Pocc1* 104 128 Pau7 105 111 -- Jolene Sutton PhD candidate Department of Zoology University of Otago 340 Great King St. PO Box 56 Dunedin 9054 New Zealand Fax: (64...

...quot;peso" de 0.5, porque si hay sobredominancia, dominancia, etc ..., aunque desconozco el caso en particular. Javier Rubén Marcuzzi El 11 de abril de 2015, 11:52, Jorge I Velez <jorgeivanvelez en gmail.com> escribió: > Gemma, > > Tiene que ver con cuantos alelos hay en cada locus. Generalmente esto > se codifica como 0, 1 y 2, pero los autores optaron por una codificacion 0, > 0.5 y 1 (que corresponde a tener 0, 1 o 2 alelos, respectivamente, en > el locus de interes). Asumiendo un microsatelite con alelos "A" y "a", por > ejemplo, 0 corres...

Hi , is it possible to calculate ld-measures D, D', r and perhaps corresponding p-values with r IF THE PHASE IS KNOWN? The genetics - package provides the LD function only for ambigious phase. Thank you very much Bettina Kulle