Hello,
I've a big problem with snp function.
I must use it in first step of my analysis. If I use example of alleles (find -> https://www.rdocumentation.org/packages/SNPassoc/versions/2.0-11/topics/snp) everything is ok but if I use my data R give me error Error in snp(test, sep = "") : SNP must have only two alleles.
I check my data and it's the same class (character). Both datasets look the same.
test - my data
dat2 - example
I don't know what I've to do now... Please help.
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written
by
gosssheen •
Read the documentation and understand your situation. For a biallelic diploid locus, there can only be 3 possible unphased configurations: HOM-REF, HET and HOM-ALT. Your "test" dataset has all 4 nucleotides, so obviously it's not a SNP at a single locus but a collection of SNPs - meaning, not all 10 configurations are possible at the same location.
Contrast this to dat2 where the only 2 alleles are A and G. Either change your dataset so it's compatible or use sapply(test, snp, sep = "") to get 10 SNP objects (not a meaningful thing to do)
Now, I understand, thanks :)
But I have one more question. It's my sample of individuals and I've got more than two alleles. For examples in E1 are C,G and A. What should I do with this problem?
Yes, I tried and R shows me a error "SNP must have only two alleles"
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