[adegenet-forum] Include population info in genlight object

[Jombart, Thibaut]

Hello, 

yes, the problem is that you left the first column reading 913,914, etc. meaning as many copies of second allele. There is no limitation as to the ploidy of the data in genlight objects, and this is a pretty good illustration.

You need to provide the constructor (new) with a matrix of nb of alleles ONLY as first argument; for instance:
###
x<- new("genlight", SNPmerge[,-(1:3)], indNames = SNPmerge$sampleName, pop = SNPmerge$PopID, ploidy=2)
###

Hope this helps.

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 Linda Rutledge [lrutledge at trentu.ca]
Sent: 16 September 2011 19:31
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Include population info in genlight object

Hi,

I have managed to subset my 48K SNP data and retrieve both a pca and tree. However, I have now included population ID information in a column and I would like to plot individuals in the pca coloured and clustered by population.  (As shown in section 5.2 of "practical-day1.1.2" of the adegenet documents). I think the issue may be with telling the genlight object where the population information is:

#show rows 1-5 and columns 1-5 of merged file of SNP genotypes and Sample Name (sampleName) and Population ID (PopID)
> SNPmerge[1:5, 1:5]
  Order sampleName PopID chr1.100091560 chr1.100112448
1     1      dog89     3              0              2
2     2      dog93     3              2              1
3     3     dog858     3              0              2
4     4     dog859     3              0              1
5     5     dog860     3              0             NA

# take a subset of SNPmerge
>SNPmergeSub <- SNPmerge[913:1013, 1:20]

show rows 1-5 and columns 1-5 of subset

> SNPmergeSub[1:5, 1:5]
    Order sampleName PopID chr1.100091560 chr1.100112448
913   913    MIDcla1     8              0              2
914   914    MIDcla2     8              1              0
915   915     Necla1     9              0              1
916   916     Necla2     9              0              1
917   917   WESTcla1    11              0              0

#remove column "Order" from subset
>SNPmergeSub$Order = NULL

#create genlight object from subset with individual names and population
> x<- new("genlight", SNPmergeSub, indNames = SNPmergeSub$sampleName, pop = SNPmergeSub$PopID)
> x
 === S4 class genlight ===
 101 genotypes,  20 binary SNPs
 Ploidy statistics (min/median/max): 913 / 963 / 1013
 189 (0.09 %) missing data
 @pop: individual membership for 7 populations
 @loc.names: labels of the SNPs


So there is something wrong here because my ploidy should be 2.

Thanks.
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