[adegenet-forum] SNP genotype codes input

Jombart, Thibaut t.jombart at imperial.ac.uk
Fri Mar 14 16:48:33 CET 2014

Hi there, 

this is quite close the one of the possible input to get genlight objects. See the vignette on 'genomics':

(in current adegenet version)

(in release 1.4-0, on CRAN imminently, though tutorial will take a couple of more days)

From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of karim karimi [karim.karimi81 at gmail.com]
Sent: 12 March 2014 17:07
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] SNP genotype codes input

Dear all
 I am working on SNPs genotypes data set that was related to 600,000
 snp sites in 100 individuls.  i found that "adegenet" package
 have many useful functions that we are searching them but i
 dont know if i can use this package for my analyse: i have a text
file included 0,1,2 and 9 codes that show AA,AB,BB and NA  (missing
 data) genotypes respectively. SNP in rows and individuls in columns:

          indivi1    indivi2 ............................................
 snp1    0            1         9      2      0
 snp2    1            1         0      9      9
 snp3    0            0         9      9      1
how can i change the format of my data in adegenet input format ( what
codes should be replaced) and can "adegenet" do analyse process for
huge data set ?


Karim Karimi
Ph.D Candidate of Animal Breeding & Genetics
Department of Animal Science,
College of Agricultural Science,
Shahid Bahonar University of Kerman, Iran

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