similar to: How to create a chromosome location map by locus ID

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:

Please forgive the cross posting. I sent this to Medstats and have not received any response. I am looking for a good written explanation of components of variance (a.k.a variance components), in particular as they are used in genetic analyses. Does anyone have a suggestion? I am interested in books, articles and on-line material. I intent to give the material to some of my students none of whom

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

Dear ALL: How I show the area under the normal curve for example for the following example: Assume X has N(100,15). How to show the area corresponding to the probability: P(90<X<110) With many thanks Abou ========================== AbouEl-Makarim Aboueissa, Ph.D. Assistant Professor of Statistics Department of Mathematics & Statistics University of Southern Maine 96

Un saludo: Estoy intentando con el comando "detach()" eliminar todos los archivos que durante la analíticas voy utilizando y "attached" al programa. El problema es que usando detach () no me borra todo lo adjuntado. No sé si estoy usando mal el comando o estoy usando un comando incorrecto que no es para esto. Gracias. Juan Bautista Relloso Barrio Técnico del Dpto

Buenas, En R, como en la mayoría del software estadístico, no se utiliza ningún nivel de confianza sino que lo que se calcula es el p-valor asociado al contraste. De forma que cuanto más cerca de 0 esté el p-valor "menos credibilidad le damos a la hipótesis nula". Dicho mejor, debemos rechazar la hipótesis nula si el p-valor está por debajo de nuestro nivel de confianza. Por ejemplo,

Hola a todos: Preguntar si alguien sabe si se puede conectar el Tinn-R con la versión 2.15 de "R" Yo lo he intentado y no lo consigo. si abro un script con el tinn-R no se me activan los botones para poder correr las lineas y que el resultado aparezca en la ventana de abajo de "R". Vamos como pasaba con la versión 2.14 Sin más un saludo a todos y gracias por

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

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

#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,

Buenas tardes. Tengo un ensayo de dos factores (Variedad y dosis) Quisiera hacer anovas para cada una de las dos variedades que estoy evaluando. Lo puedo hacer cogiendo los datos primero de una variedad y luego de la otra. Pero creo que hay un comando "by variedad" que lo hace si necesidad de andar modificando el archivo de datos. Pero no sé dónde hay que colocarlo. Si alguno me puede

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

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

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

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, 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

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

Buenas tardes, Estamos intentando hacer un estudio sobre diversidad en gatos callejeros ('stray cats') de la base de datos 'nancycats' (librería 'adegenet') de R. Sin embargo, no entendemos muy bien los datos. ¿Alguien puede explicarnos a qué corresponde la variable respuesta? Entendemos que las filas son los 237 gatos (observaciones), y las columnas se corresponden con

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'

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