[R-sig-genetics] Query regarding DAPC using ADEGENT in R

[Bhuller, Ravneet]

It’s all working now.

Thanks, Thibaut.

Regards,

Rav



On 2 Sep 2016, at 10:24, Thibaut Jombart <thibautjombart at gmail.com<mailto:thibautjombart at gmail.com>> wrote:


Hi there,
Please check carefully the error msg. Here the problem is stated clearly. You either need to provide the group factor as argument to dapc, or to attach it to the object - pop(x) <- ...

Cheers
Thibaut

On 2 Sep 2016 09:51, "Bhuller, Ravneet" <ravneet.bhuller13 at imperial.ac.uk<mailto:ravneet.bhuller13 at imperial.ac.uk>> wrote:
Hello Thibaut,

The genind object is of size 8.9 Mb.

Yesterday, when I tried find.clusters in the Rmarkdown document, it did not ask for any input. I wanted to know how many components to retain to run DAPC.

However, today, when I tried find.clusters in R (without Rmarkdown), it worked absolutely fine.

But another problem is that pop function is giving an error. Attached is the screenshot. My data is DNA multiple-sequence-alignment FASTA files of 357 genes, which are concatenated. Each file has same 220 bacterial strains. And my meta data includes 220 strains distributed into 19 serovars (integers). Is my meta data in the correct required form?

<DAPC ERROR.png>

Kind regards,

Rav




On 1 Sep 2016, at 16:17, Thibaut Jombart <thibautjombart at gmail.com<mailto:thibautjombart at gmail.com>> wrote:

Hi,

what is the size of the dataset? Are you sure it did not display a graph of
cumulative variance and waits for your input? As you specified it, the
function is interactive and will wait on your input before giving results.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR <https://twitter.com/TeebzR>


On 1 September 2016 at 00:33, Graham Reynolds <greynold at unca.edu<mailto:greynold at unca.edu>> wrote:

Hi Rav, if you have multiple cores on your CPU you can distribute the task
among them, which really speeds it up. That might at least let you see
whether it is a problem with the dataset.

grp <-find.clusters(app, max.n.clust=n, parallel = "multicore", ncpus = 4)

You might need to install the Parallel package

Cheers


R. Graham Reynolds, Ph.D.
Assistant Professor of Biology
University of North Carolina Asheville
www.caribbeanboas.org<http://www.caribbeanboas.org/>



*From:* R-sig-genetics <r-sig-genetics-bounces at r-project.org<mailto:r-sig-genetics-bounces at r-project.org>> on behalf of
Bhuller, Ravneet <ravneet.bhuller13 at imperial.ac.uk<mailto:ravneet.bhuller13 at imperial.ac.uk>>

*Sent:* Wednesday, August 31, 2016 5:39 AM
*To:* r-sig-genetics at r-project.org<mailto:r-sig-genetics at r-project.org>
*Subject:* [R-sig-genetics] Query regarding DAPC using ADEGENT in R

Dear All,

I am trying to do DAPC on my genind object (app) using ADEGENET in R. But
when I run the following command:

grp <- find.clusters(app)

it is processing continuously for more than 2 hours but not producing any
output. Any guidance will be very much appreciated.

Regards,

Rav

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