Does anyone use the R library GenABEL? I am using it to calculate SNP
interactions.
I have a list of 100 SNPs, I need to look at the interaction between each of
two SNPs among the list. my question is how to perform this in GenABEL. I
want to use the "lm" function, but don't know how to use the SNP
information.
for example:
result <- (lm(y~SNP1+SNP2+SNP1*SNP2))
the problem here is the "SNP1,SNP2" are not working in this place,
because
it's not a right format to use the SNP information stored in the GenABEL
library. Someone said I could first import the GenABEL format genetic data
to the format used by "genetics" library by using as.genotype. I
tried, but
seems it does take a long time, and the transformation has been running for
about 18hs, but it is still running, I don't even know if the transformation
is doable.
anyone has any idea about how to deal with this problem.
thank you very much!
karena
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