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SNPs 0,1,2 #24
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Hi David, you can omit the minor allele from the column names by creating the BEDMatrix object using Hope that helps, |
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) 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) |
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
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