[R] R: estimating genotyping error rate

Hello, I have SNP data from genotyping. I would like to estimate the error rate between replicated samples using R. How can I proceed? Thanks Meriam __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listin

Re: [R] R help: fviz_nbclust’ is not available (for R version 3.5.2)

provides a > clear error message that can be a reminder to the user to install the package. > > Execute your code line by line and solve the first error you encounter by > examining the error message and reviewing what that line of code is designed > to do. > > On January

[R] R help: fviz_nbclust’ is not available (for R version 3.5.2)

Hello, I'm struggling to install a function called "fviz_nbclus". My code is the following: pkgs <- c("factoextra", "NbClust") install.packages(pkgs) library(factoextra) library(NbClust) # Standardize the data load("df4.rda") library(FunCluster) install.packages("fviz_nbclust") #fviz_nbclust(df4

Re: [R] Fwd: Overlapping legend in a circular dendrogram

coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Fri, Jan 11, 2019 at 12:47 PM N Meriam wrote: >> >> Hi, I'm facing some issues when generationg a circular dendrogram. >> The

[R] Fwd: Overlapping legend in a circular dendrogram

Hi, I'm facing some issues when generationg a circular dendrogram. The labels on the left which are my countries are overlapping with the circular dendrogram (middle). Same happens with the labels (regions) located on the right. I run the following code and I'd like to know what should be changed i

[R] Overlapping legend in a circular dendrogram

Dear all, I run the following code and I get this graphic (Imageattached). What should I change in my code in order to adjust the overlapping objects? load("hc1.rda") library(cluster) library(ape) library(dendextend) library(circlize) library(RColorBrewer) labels = hc1$labels n = length(labels)

[R] R help: circular dendrogram

Dear all, I generated a circular dendrogram with R (see attached). I have a total of 360 landraces. What I want to do next is generate a different color for each cluster and also generate colors to show the country/region. I don't know if it's also possible to put a code number (associated with ea

Re: [R] Warning message: NAs introduced by coercion

-- > David L. Carlson > Department of Anthropology > Texas A&M University > > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of N Meriam > Sent: Tuesday, January 8, 2019 1:38 PM > To: Michael Dewey > Cc: r-he

Re: [R] Warning message: NAs introduced by coercion

gt;G-7:A>G" "2" "0" "3" "0" > > [3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0" > > [4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0" &g

Re: [R] Warning message: NAs introduced by coercion

ot;> class(genod2)[1] "matrix" > # read data > filn <-"simTunesian.gds"> snpgdsCreateGeno(filn, genmat = > genod,+ sample.id = sample.id, snp.id = snp.id,+ > snp.chromosome = snp.chromosome,+ snp.position

[R] Warning message: NAs introduced by coercion

Dear all, I have a .csv file called df4. (15752 obs. of 264 variables). I apply this code but couldn't continue further other analyses, a warning message keeps coming up. Then, I want to determine max and min similarity values, heat map plot, cluster...etc > require(SNPRelate) > library(gdsfmt) >