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andreyshabalin / MatrixEQTL

Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
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Multiallelic variants #15

Closed Tijs-dot closed 3 years ago

Tijs-dot commented 3 years ago

Dear Dr. Shabalin,

I amtrying to perform an eQTL analysis using your tool, using genotypes obtained for HLA genes. These genes have many different possible alleles, which makes annotating them with either 0,1 or 2 problematic.

Is there a way to input such multiallelic variants in MatrixEQTL?

Kind regards, Tijs

andreyshabalin commented 3 years ago

What would be the linear model you'd like to estimate with such data?

Tijs-dot commented 3 years ago

Simple linear regression with additive effect. I have just under 90 samples for which I have obtained genotypes and gene expression data, and I have their covariate data as well.

andreyshabalin commented 3 years ago

Sorry, Matrix eQTL doesn't support such analysis.