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MRCIEU / TwoSampleMR

R package for performing 2-sample MR using MR-Base database
https://mrcieu.github.io/TwoSampleMR
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Clarification - incompatible allele #102

Open jonnyrose opened 5 years ago

jonnyrose commented 5 years ago

Can you clarify what "incompatible allele" means versus ambiguous, palindromic (inferrable), palindromic (not inferrable) or incompatible allele frequencies?

Removing the following SNPs for incompatible alleles: rs11689269, rs12682297, rs2992632, rs4493682, rs55830725, rs6799130, rs7131944, rs7955289

In each of the above snps so removed, the effect and other alleles aligned. What further information from the dataset is being used to determine "incompatible alleles"?

Thanks in advance.

mightyphil2000 commented 5 years ago

Could you send the code that produce the above error or send a snapshot of the SNPs and their respective effect and non effect alleles in the exposure and outcome datasets?

Incompatible allele reflects a difficulty in aligning the exposure and outcome datasets to the same effect allele.

llalluan commented 8 months ago

Can you clarify what "incompatible allele" means versus ambiguous, palindromic (inferrable), palindromic (not inferrable) or incompatible allele frequencies?

Removing the following SNPs for incompatible alleles: rs11689269, rs12682297, rs2992632, rs4493682, rs55830725, rs6799130, rs7131944, rs7955289

In each of the above snps so removed, the effect and other alleles aligned. What further information from the dataset is being used to determine "incompatible alleles"?

Thanks in advance.

According to my understanding based on the harmonise.R script and the data used to test, "incompatible allele" means an allele with the same chromosome, RSID, and position, but with different A1 and A2 in exposure data and outcome data. For example, a SNP rs1146883 ( chromosome:13, position:76885019) appears in both exposure data and outcome data, but A1 and A2 are [C,A] in exposure data, while they are [T,A] in outcome data. These information about the SNP rs1146883 are "incompatible", and thus could not be treated as the same allele and could not be used to perform MR analysis.