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francois-a / fastqtl

Enhanced version of the FastQTL QTL mapper
GNU General Public License v3.0
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Imputing missing phenotypes #19

Open zmy24 opened 3 years ago

zmy24 commented 3 years ago

Hi, I have a phenotype data with some missing value. And I found the Fastqtl will impute the issing phenotypes automatically. I wonder if it was imputed by the average value? And how can I avoid imputation?

francois-a commented 2 years ago

Yes, missing phenotypes are mean-imputed. To avoid this, you either need to filter out phenotypes with missing values, or impute them using an alternate method prior to running fastQTL.