[adegenet-forum] importing data NA coding

[Jombart, Thibaut]

Dear Evelyne, 

"0000" are well interpreted as NAs when reading nancycats data in genpop format.

The head of the file reads:
#######################
Genotypes of cats from 17 colonies of Nancy (France)
fca8
fca23
fca43
fca45
fca77
fca78
fca90
fca96
fca37
Pop
1, 0000 0409 0404 0103 0909 0306 0909 0808 1010
1, 0000 0909 0407 0305 0909 0306 0209 0808 1010

#######################

Import into R:
#######################
> example(read.genepop)
[...]
> genind2df(obj)
    pop fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
1     1 <NA>  0409  0404  0103  0909  0306  0909  0808  1010
2     1 <NA>  0909  0407  0305  0909  0306  0209  0808  1010
#######################

If you are using an outdated version of adegenet, please try with the latest stable version. If the problem persist, can you please send me an example data file so that I can try to reproduce and fix the issue?

Cheers

Thibaut

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Evelyne Heyer [heyer at mnhn.fr]
Sent: 25 May 2011 13:53
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] importing data NA coding

When I import data from Genepop file with the read.genepop function, the
missing data frrom Genepop ("0000" allele) are not coded as NA in
genpop. How to solve this problem?
Evelyne Heyer


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