adegenet

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cross validation is slow

3

Hello, Forgive the generality of the title. I have a DAPC cross validation running on a dataset of approx 400 samples x 5000 loci. The cross validation is testing values...

pdimens

Hello, I have successfully managed to run an spca but am having issues when I attempt to plot the results. All 6 displays are visible (connection network, the three score...

z-j-r

pairwise.fast(sim2pop) function not working ?

7

I'm trying the data analysis provided in the adegenet2.1.0 manual. https://raw.githubusercontent.com/thibautjombart/adegenet/master/tutorials/tutorial-basics.pdf The particular function is not working - pairwise.fast(sim2pop) Its says, Error in pairwise.fst(sim2pop) : could not find function "pairwise.fst"...

sunnyEV

Remove exportPattern() from NAMESPACE

1

At the moment, we are using this as a kludge to export all of the functions that don't start with a dot and it's not a good practice because it...

zkamvar

121 of 9,346 importing from structure file - inconsistent "negative subscripts" error

15

Hi, I am trying to run DAPC on my new Sceloporus dataset. I successfully got this to work before with some other datasets. I am using adegenet 2.0.0. When I...

gottschoa

[help wanted] cannot use multi-cores when dealing with genlight

3

Hi, I have a data set of about 2600 individuals and 150, 000 SNPs for each individual. When I run read.PLINK or glPCA with parameter [parallel = require("parallel" )] on...

yanchunzhang

glPca and dapc freezing -- am I picking the wrong nf?

1

Hi all, I'm coming to an issue with running both glPca() and dapc(), where in both cases it seems as though RStudio is freezing. I can't figure out if I...

konradtaube

I want to run DAPC on a large SNP alignment so I first ran glPca on my fasta file. I then tried passing the PCA scores to find.clusters, and the...

nicolettacommins

add support for parallel in find.clusters

2

I did the same as in `glPca` (that is, I used `parallel::mclapply` and added the arguments `parallel` and `n.cores`). I also updated the documentation and `DESCRIPTION`.

timflutre

legend disappear when i export pdf

1

hello i had use _"adegent"_ finished my analysis and it works good however，when i want to export my results figures in _pdf_，i find that the legend of the picture is...

zxy1555847