How to handle the missing dosages?
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Hi Predixcan guys,
How to handle the missing dosages, while creating the predixcan format dosage files ? If its 'NA', the script throws error saying cannot convert string to float NA.
Thanks
Veera
Hi Veera
The best option is to impute the genotype and not have the NA. A very
simple though not optimal is to impute with the mean of the population.
HTH
Haky
On Thursday, November 3, 2016, Veera notifications@github.com wrote:
Hi Predixcan guys,
How to handle the missing dosages, while creating the predixcan format
dosage files ? If its 'NA', the script throws error saying cannot convert
string to float NA.
Thanks
Veera—
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Hi Haky,
Thanks for the quick response. I guess that's what the convert_plink_to_dosage.py does, right ? (I see that the script replaces NA with MAF*2.
-Veera