[adegenet-forum] importing annex information within the Genind object (@other)

[Thibaut Jombart]

Hi Michaël,

This question is quite common, so thanks for your post. Miscellanous 
information can be stored inside the @other slot of genind/genpop 
objects. If there is a single population factor, it is better to have it 
stored in @pop, since this will be used automatically by several 
functions. The same is true for spatial coordinates, expected to be in 
@other$xy.
> Dear Thibaut,
>
> I am Michaël, I have a problem with Adegenet when I want to import my 
> dataset from a data.frame. The problematic point is to import annex 
> information within the Genind object. I am not very use to that kind 
> of object. Specifically my data are imported in R as a data.frame ( 
> read.table() ), and I would like to add information within the Genind 
> object, such as the population, the geographic coordinates, and other 
> factors, such as the year.
>
> Here is an example of the kind of script I am using:
>
>> #My data
>> ampelo_gp<- cbind(AQmalus3, AQmalus4, AQmalus8, AQmalus10, AQmalus11)
>> head(ampelo_gp)
>> ampelo_ID <- cbind(ID, DNAsamples,Populations,X,Y, Country, Year)
>> head(ampelo_ID)
>>
>> #the Genind object
>> amp_ade <- df2genind(X=ampelo_gp, ind.names=ID, pop=Populations, 
>> ploidy=1)
>> amp_ade at pop=Populations    #it works, but is this the best way to 
>> proceed?
>>
>> #here I am trying to add annex information in the  class @other est 
>> définie comme NULL.
>> amp_ade at other@xy=cbind(X,Y)
>> amp_ade at other@coutry=Country
> Here this doesn't work, R return that "amp_ade at other" is defined as NULL.
> How can I  import these information within the @other?
>
What is tricky here is that there is a mix between S4 object, whose 
slots are accessed by '@', and a S3 object (a list), accessed using '$'. 
For instance:
##
 > example(df2genind)
 > obj at other
NULL
##
to add smthg to obj, the right use is:
##
 > obj at other$foo <- "Here is a component of the list 'other'"
 > obj at other
$foo
[1] "Here is a component of the list 'other'"
class(obj at other)
##

- obj at other refers to a slot called 'other' of an S4 object
- obj at other$foo is a component of the list 'obj at other'.

Note that in adegenet, there is an emulation of @ into $, so you can 
just use $ everywhere:
##
 > obj$other$toto <- "yop yop yop"
 > obj$other
$foo
[1] "Here is a component of the list 'other'"

$toto
[1] "yop yop yop"

 > identical(obj$other, obj at other)
[1] TRUE
##

Best regards,

Thibaut.

-- 
######################################
Dr Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
jombart at biomserv.univ-lyon1.fr
http://biomserv.univ-lyon1.fr/%7Ejombart/
http://adegenet.r-forge.r-project.org/