search for: adegenet

Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function provide in adegenet package). After convert my file the pairwise.fst function is not found. If you could help me would be great. Greetings: Rui Oliveira -- -----------...

Dear R developers, I am having a slightly weird issue with a S4 method defined in my package adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the code implementing the method has not changed for more than a year and worked well so far. The problem is the following. I define, in the package, a method "[" for the S4 class 'genind'. The method's definitio...

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 los 9 microsatélites (¿dentro de los que hay las 17 colonias de gatos?) Pero...

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 ..., aunque desconozco el caso e...

Hi, I am trying to calculate Moran's I test for the residuals for a regression equation, but I have trouble converting my coordinates into nb format. I have used the dnearneigh() funtion now with an arbitrarily high upper distance to make it include all plots. However, when I do the lm.morantest() I get a Moran's I value which is the same as the expected value and a P-value of 1. I

...5+SAMPS:ncol(Mydata))] locus # Locus1 Locus2 Locus3 # Samp1 GG <NA> GG # Samp2 AG CA GA # Samp3 AG CA GG # converts geno matrix to genind object (adegenet) Mydata1 <- df2genind(locus, ploidy = 2, ind.names = ind[1:SAMPS], pop = population[1:SAMPS], sep="") Mydata1$tab # get stats on newly created genind object # Locus1.G Locus1.A Locus2.C Locus2.A Locus3.G Locus3.A # Samp1 2...

...95 95 43 > e-mail: Roger.Bivand at nhh.no Basically, Monmonier algorithm aims at finding maximum-difference boundaries between geo-referenced objects. It requires a set of georeferenced objects along with matrix of distances among these objects. Monmonier algorithm is now implemented in the adegenet package (http://pbil.univ-lyon1.fr/software/adegenet/). Main functions are 'monmonier' and 'optimize.monmonier'. Despite the package is devoted to genetic data analysis, these functions can handle other kind of data as well. The main difference I can see between this implement...

Hi, I am a new student to R and I was hoping someone could help me with the error message I keep getting when I try to use the nb2listw() function. I have 45 sites and I want to get an autocorrelation value for sites within 1000m of each other. coords<-cbind(EAST,NORTH) coords<-as.matrix(coords) nb1000<-dnearneigh(coords,0,1000,longlat=TRUE) then when I try to run the

...he package in which the appropriate method is defined is loaded automatically when calling the method. The problem is that if the package is indeed loaded automatically, the appropriate method is not used. An example using the package pixmap (but I obtained similar results with S4 objects from adegenet and phylobase packages): ##### in one R session > library(pixmap) > foo <- new("pixmap") ## here the object is printed with the appropriate show method. > foo Pixmap image Type : pixmap Size : 0x0 Resolution : 0x0 Bounding box : 0 0 0 0 > setClass("myClass",...

...Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health St Mary?s Campus Norfolk Place London W2 1PG United Kingdom Tel. : 0044 (0)20 7594 3658 t.jombart at imperial.ac.uk http://sites.google.com/site/thibautjombart/ http://adegenet.r-forge.r-project.org/

I am trying to use the cca/rda/capscale functions in vegan to analyse genetic distance data ( provided as a dist object calculated using dist.genpop in package adegenet) with geographic distance partialled out ( provided as a distance object using dist function in veganthis method is attempting to follow the method used by Geffen et al 2004 as suggested by Legendre and . FORTIN (2010). I cannot see how to introduce the Conditioning ( partialled) second dist...

...ntaining 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(). A piece from the dataset is displayed further below. Here my code: /Code/ library("ape") library("adegenet") library("pegas") / load with no problem. / /the command: / > data.loci <- read.loci(file ="/Users/victor/Documents/SIV_Compartment/data/pegas_data_seq.txt", header = TRUE, col.loci = seq(1,200), col.pop = TRUE) /seems to work./ /in fac...

Hi, I have collected data on trees from 5 forest plots located within the same landscape. Data within the plots are spatially autocorrelated (calculated using Moran's I). I would like to do a ANCOVA type of analysis combining these five plots, but the assumption that there is no autocorrelation in the residuals is obviously violated. Does anyone have any ideas how to incorporate these spatial

I get tables with millions of rows. For plotting to a screen-size jpg, obviously just about 1000 points are enough. Instead of feeding plot() the original millions of rows, I'd rather shrink the original dataframe, using some kind of the following interpolation: -- split dataframe into chunks of N rows each, e.g. 1000 rows each -- compute average for each column -- issue one new row

I was running a sampling syntax based on a data frame (ago) of 160 rows and 25 columns. Below are the column names: > names(ago) [1] "SubID" "AGR1" "AGR2" "AGR3" "AGR4" "AGR5" "AGR6" "AGR7" "AGR8" [10] "AGR9" "AGR10" "WAGR1" "WAGR2"

Dear all, (Mac OS X 10.4.11, R 2.6.0) I have a quantitative dataset with a lot of Na?s in it. So many, that it is not possible to delete all rows with NA?s and also not possible, to delete all variables with NA?s. Is there a function for a principal component analysis, that can deal with so many NA?s. Thanks in advance Birgit Birgit Lemcke Institut f?r Systematische Botanik

Hi everyone, I have a matrix that contains 1000 replicates of a sample of a list of values. I want to group each row (row=replicate) into my defined bin ranges and then calculate the mean and stdev for each of the bin ranges (so I will have 1000 rows but ncol=number of bin ranges). I don't know how to group rows in a matrix matrix according to another vector (which is what I think I need to

Dear R user, I am using Sweave to write my reports with R code. Unlucly my code take a lot of time to run, and I don't want to run it multiple time, if possible, as I am still developping the tools. It seems that a sweave run does not save the enviroment at the end of the process, is there a way to avoid to lunch multiple time the same commands? maybe it could be possible to store chunck of

Hi the list, I am defining a new class MyClass. Shortly, I will submit a package with it. Before, I would like to know if there is a kind of "non official list" of what method a new S4 object have. More precisely, personnaly, I use 'print', 'summary' and 'plot' a lot. So for my new class, I define these 3 methods. Is there some other method that a R user can

Hi Everyone, I am doing a project based on "Spatially Lagged Predictor Variable Models", I would like to know which package in R would execute this model. Also, I am new to this field of spatial statistics. Any suggestions for a good book on spatial regression analysis would be appreciated. Thanks Again. Cheers Arun -- View this message in context: