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I want to create a MDS plot with pairwise Fst values derived from a population genetics project. My Fst values are in a tab-delimited file (lower triangle only) that I view with Excel. When I use the cmdscale command I get the message: Error in cmdscale(x) : Distances must be result of dist or a square matrix In addition: Warning messages: 1: "^" not meaningful for factors in:

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

# 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

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

My question is with respect to mCLUST and the values of BIC and log likelihood. The relevant part of my R script is: ######################### BEGIN MDS ANALYSIS ######################### #load data data <- read.table("Ecoli33_Barry.dis", header = TRUE, row.names = 1) #perform MDS Scaling mds <- metaMDS(data, k = Dimensions, trymax = 20, autotransform =TRUE, noshare = 0.1,

Version 0.2 of the package LDheatmap is now on CRAN. The main function LDheatmap produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The revisions to the package are aimed at improving the user's ability to modify and annotate the

Hello, I have some patient data for my masters thesis with three groups (n=16, 19 & 20) I have completed compiling the results of 7 tests, for which one of these tests the variances are unequal. I wish to perform an ANOVA between the three groups but for the one test with unequal variance (<0.001 by both bartlett and levene's test) I am not sure what to do. I thought i would run

Dear R wizards, I am seeking advice on graphics in R. Specifically, how to manipulate the size and save a plot I have produced using the LDheatmap library. I confess I am relatively new to graphics in R, but I would greatly appreciate any suggestions you may have. LDheatmap produces a coloured triangular matrix of pairwise associations between 600 genetic markers in my dataset.

Hello, I've used mantel tests a fair bit for standard genetic/geographic/landscape analyses. I realize it involves permutations of rows and columns in the matrix to obtain correlation coefficients. However, for a certain question, I am interested in populations that are nearest neighbours to each other, and identifying factors that affect genetic distance between them. So because of

Hello, I have a unconventional question arising from my current master thesis on regression modeling. Suppose we have fitted a (linear) relationship between a dependent variable y and an independent variable x. Now we choose two points on the x-axis, i.e. according to percentiles x10 and x90. These two points are chosen to select the data points for two groups in order to perform pairwise

Dear useRs, In a thesis, I found a mention of the use of pairwise deletion in linear regression and GLM (binomial family). The author said that he has used R to do the statistics, but I did not find the option allowing pairwise deletion in both lm and glm functions. Is there somewhere a package allowing that ? Thanks, Arnaud [[alternative HTML version deleted]]

Hi, (Sorry for the cross-posting.) After manually installing the 32-bit libjack packages on my 64-bit system, the original problem ("Can't connect to JACK") is gone; now I get a whole new set of errors instead :) When I try to start the Kontakt 5 VST from festige (via fst, via WINE), this is what I get: ============================ ----------------yo... lets see...

Hello everybody. I wrote a small patch in order to support what I think is an absolutely needed feature in order to make rsync-based backups retaining complete ownership permission when writing to an opensolaris machine using --fake-super. My goal is making backups of linux boxes to opensolaris/zfs. In order to make it work just do patch -p1 < patch_file.txt inside rsync source tree. and

R-List, I'm trying to compute pairwise distances among pairs of observations, which each pair containing data from 2 groups. There are more than 100000 unique pairs. I have programmed a distance function that has three parameters, a vector of covariates from the ith observation in Group 1, a vector of covarites from the jth observation in Group 2, and a weighting matrix. I have used

Add install_file_to_device() to support unmounted ext2, ext3 and ext4 filesystem. Usage: $ extlinux -i /dev/sdXN or $ extlinux -i file_block We don't need any new options, it will check whether the target is a directory or device and decide what to do, it would stop and error if the device is mounted. More info: * It will use libext2fs to read and write the file. * It will be used when the

Dear R Helpers I am having difficulty understanding how to use the penalty matrix for the nomROC function in package 'nonbinROC'. The documentation says that the values of the penalty matrix code the penalty function L[i,j] in which 0 <= L[i,j] <= 1 for j > i. It gives an example that if we have an ordered response with 4 categories, then we might wish to penalise larger

Thank you very much Louis, Rowland, Mike ! I have made all the changes proposed by Louis but still have the same problem. -> kinit works now with /var/lib/samba/private/secrets.keytab ------------------------ ~# kinit -k -t /var/lib/samba/private/secrets.keytab FICHDC$ ~# ------------------------ -> but samba-tool authentication with machine account fail : ------------------------ ~#

Hallo List, I'm trying to implemement a restricted permutation scheme in permutest(). More precisely I have dependence in my data that should be allowed for in the permutation - I simulated the problem in the example of the vegan documentation p.24: library(vegan) data(varespec) ## Bray-Curtis distances between samples dis <- vegdist(varespec) ## First 16 sites grazed, remaining 8 sites

Hello thanks again for the help ! I have analysed samba logs more closely. I'am very worried. I have three DC (fichdc, fichds01, fichds02) but here I talk just about fichdc's logs. -> Almost every times, "AS-REQ" fail for the 3 DCs with something like this : ---------------- Kerberos: AS-REQ FICHDC$@NET.LYC-GUILLAUME-FICHET.AC-GRENOBLE.FR from ipv4:172.16.0.20:59818 for

Hai, Before you start, Backup, /etc/ /var/lib/samba better safe than sorry.. Stop samba and related services ( check it at least nmbd smbd winbind samba samba-ad-dc) > -----Oorspronkelijk bericht----- > Van: samba [mailto:samba-bounces at lists.samba.org] Namens > Prunk Dump via samba > Verzonden: woensdag 21 juni 2017 11:57 > Aan: samba at lists.samba.org > Onderwerp: