[adegenet-forum] SNP genotype codes input

karim karimi karim.karimi81 at gmail.com
Wed Mar 12 18:07:50 CET 2014

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


More information about the adegenet-forum mailing list