[adegenet-forum] lost in the manual

[Jombart, Thibaut]

Dear Marina, 

I'm pleased to know things are getting better.There is a syntax error in your command line:
CM <- read.structure(file "CMinput.str"), n.ind=151, n.loc=9,
should read:
CM <- read.structure(file="CMinput.str", n.ind=151, n.loc=9,  # ... etc.

So far, there is no special handling of null alleles in adegenet. I guess most input files would indicate null alleles by NAs, at least in the case of microsatellites.

Best regards,

Thibaut. 
________________________________________
From: mchiappero at efn.uncor.edu [mchiappero at efn.uncor.edu]
Sent: 12 January 2010 16:46
To: Jombart, Thibaut
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: RE: [adegenet-forum] lost in the manual

Dear Thibaut:

Well, things are getting better, thank you for your advice.
Unfortunately I need more of it.
I was able to read the "nancycats.str" file using read.structure and
to reproduce some of the analysis in the manual and tutorial. However,
when I try to use my own input file, I get this error message:

> CM <- read.structure(file "CMinput.str"), n.ind=151, n.loc=9,
> onerowperind=TRUE, col.lab=1, col.pop=2, row.marknames=1, ask=FALSE,
> missing=NA)

Error en strsplit(char, "[.]") : argumento de tipo no-carácter
[translation:
Error in strsplit(char, "[.]") : non-character type argument
or something like that, my R is in Spanish]


Can you help me? I already checked the input file for errors and it
seems to be OK. It's the same input file I already used with
Structure, except that I removed the row indicating loci with null
alleles.
Speaking of null alleles, I have a question. How does Adegenet deal
with null alleles?

Thank you very much for your kindness


Marina




"Jombart, Thibaut" <t.jombart at imperial.ac.uk> ha escrito:

> Dear Marina,
>
> I'm sorry to hear that you are struggling with the adegenet manual -
> it was not meant to induce such a large amount of pain in the first
> place, although I seem to understand this is an occasional
> side-effect.
>
> The package is already provided with some sample input files. These
> files usually have one of the following format: GENETIX (.gtx),
> Fstat (.dat) STRUCTURE, (.str) and genepop (.gen). These files are
> stored in the .../library/adegenet/files directory of your R
> installation. They are called upon by the function read.genetix,
> read.fstat, read.structure, etc. (see ?read.genetix).
>
> Anyway, all the instructions of the manual are meant to be
> reproducible as long as you've got the package properly installed.
> If you have specific troubles with the manual, I'd be happy to help.
>
> Best regards and happy new year.
>
> Thibaut.
>
> --
> ######################################
> Dr Thibaut JOMBART
> MRC Centre for Outbreak Analysis and Modelling
> Department of Infectious Disease Epidemiology
> Imperial College - Faculty of Medicine
> St Mary’s Campus
> Norfolk Place
> London W2 1PG
> United Kingdom
> Tel. : 0044 (0)20 7594 3658
> t.jombart at imperial.ac.uk
> http://www1.imperial.ac.uk/medicine/people/t.jombart/
> http://adegenet.r-forge.r-project.org/
>
>
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org
> [adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of
> mchiappero at efn.uncor.edu [mchiappero at efn.uncor.edu]
> Sent: 28 December 2009 13:24
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] lost in the manual
>
>  Hello!
>
> I´m trying to learn how to use Adegenet. I have a basic knowledge of
> R, but I feel so lost in the Adegenet manual... I need a lot of
> help, please!
> The first thing would be to have an input file to exercise: can
> anyone provide me a simple input matrix as an example? Maybe it
> would help me to understand the instructions in the manual.
> Thank you!
> Marina
>
> _________________________________________________________
> Marina B. Chiappero
> Genética de Poblaciones y Evolución
> Facultad de Ciencias Exactas, Físicas y Naturales
> Universidad Nacional de Córdoba
> Av. Velez Sarsfield 299
> (5000) Córdoba. Argentina
> ______________________________________________________________
>
>
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>



_________________________________________________________
Marina B. Chiappero
Genética de Poblaciones y Evolución
Facultad de Ciencias Exactas, Físicas y Naturales
Universidad Nacional de Córdoba
Av. Velez Sarsfield 299
(5000) Córdoba. Argentina
______________________________________________________________

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