Question: Loading IMPUTE2 output into R for eQTL analysis
gravatar for Alexander Skates
5.2 years ago by
United Kingdom
Alexander Skates360 wrote:

I've imputed genome-wide SNPs using the Phase 3 1000 Genomes Project data as a reference set, and I want to use this data to conduct an eQTL analysis. I want to do it in R, owing to the flexibility it affords me, and also the R package Matrix eQTL is supposedly exponentially faster than any other software with which to conduct this type of analysis.

The trouble is, I can't find any kind of post-imputation pipeline for the best method to do this. GTOOL, PLINK, SNPTEST, etc, there seem to be a variety of ways of handling the output of IMPUTE2, but I don't know what the best way for loading it into R would be.

Also, is it generally recommended to keep the files split up by chromosome or merge them into a single one?

eqtl imputation R • 2.0k views
ADD COMMENTlink written 5.2 years ago by Alexander Skates360

How you want to treat with the genotype certainity?

ADD REPLYlink written 4.4 years ago by Jimbou770
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