search for: locuse

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:

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

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

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,

My data looks like this: > data name G_hat_0_0 G_hat_1_0 G_hat_2_0 G_0 G_hat_0_1 G_hat_1_1 G_hat_2_1 G_1 1 rs0 0.488000 0.448625 0.063375 1 0.480875 0.454500 0.064625 1 2 rs1 0.002375 0.955375 0.042250 1 0.000000 0.062875 0.937125 2 3 rs2 0.050375 0.835875 0.113750 1 0.877250 0.115875 0.006875 0 4 rs3 0.000000 0.074750 0.925250 2 0.897750 0.102000

I'm trying to use a contributed package (rmetasim) to generate simulated genetic datasets. My scripts work fine when I run them on a Sun workstation running Solaris 7 and when I run them on a ~4 year old laptop PC that I have. However, when I run them on my new laptop (Dell Latitude D410 purchased in August 2005), the simulation will run for a short (variable) period of time, then R

I realized that the script I included in my original post (see below) was written for an older version of rmetasim and will not work with the current version. The only change that need be made to get my script to run with the latest release of rmetasim is to change the command 'simulate.landscape()' to 'sim.landscape()'. My apologies to anyone who tried to use my script and

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 euclidean distance is calculated: 3x3 subset used

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

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

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:

Hi everyone, I have an issue with a data conversion. First, I tried it with the reshape-package, but since it's quite a while that I used it, I feel kind of rusty... I have a data.frame like this: id Sample.Name Marker Allele.1 Allele.2 sample_id species 1 01_primer01 Dalb01 165 179

Hello, I am trying to do some simulation using the rmetasim package and I've run to this problem. --beginning of error msg-- Error in "[<-"(`*tmp*`, slice[l, ], slice[l, ], value = c(0.200000002980232, : number of items to replace is not a multiple of replacement length --end of error msg-- Here is the script I used. --script starts here-- ## load 'rmetasim'

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

Hi, I am trying to connect points on a graph that originate from *different columns of data*. For each sample I have minimum and maximum data points and I would like to draw a line connecting these in order to visualize the spread, as well as where each sample is in relation to the x-axis. So far I can generate the points, but the only lines I have been able to make join all the minimum values

Estimado Gemma Ruiz Olalla De curioso miré una búsqueda en internet, y se la comparto, de esta observe la página 8 http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf Estoy de acuerdo con Jorge y Carlos, pero por las dudas, es solo una codificación, yo sin mirar más no interpretaría que el heterocigota tiene un "peso" de 0.5, porque si hay sobredominancia, dominancia, etc

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