SNPs 0,1,2

[DavidGO464]

Hi!

I am using this snp from illumina exm1615904... whe I use plink it only uses the name of the SNP to get the geenotype (eg, as in this case normal would be CC vs GC or GG).
When usign BEDmatrix, I need to add a '_X' (underscore somthing) to the SNP name and then when I call the SNP it shows me 0,1,2, ... So I wonder what doees it means.

Kind regards

[agrueneberg]

Hi David,

you can omit the minor allele from the column names by creating the BEDMatrix object using X <- BEDMatrix(file, simple_names = TRUE). The output values are allelic dosages (0/1/2/NA), counting the number of minor alleles.

Hope that helps,
Alex

[DavidGO464]

Hi David,

you can omit the minor allele from the column names by creating the BEDMatrix object using X <- BEDMatrix(file, simple_names = TRUE). The output values are allelic dosages (0/1/2/NA), counting the number of minor alleles.

Hope that helps, Alex

Thank you for your prompt response. I think that the number is just the coding for a category regarding if it is minor allele homozygus (0: in case the variation in C>T... it would be TT; thats why is minor) and then heterozygus (eg, 1: CT) and major allele homozygus (2 : eg, CC)
i found this:

https://www.cs.cmu.edu/~sssykim/teaching/s13/slides/Lecture1.pdf

So, it would actually count the number of Major alleles (I mean, seems to be that way)