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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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Error: All samples removed due to missingness in covariate file #175

Closed SaraBandres closed 4 years ago

SaraBandres commented 4 years ago

Hi Sam,

I have a problem regarding the covariates. I would like to adjust for age at onset but I do not have that information for all the samples. How can I do? Also, if I am planning to adjust for genotypes. Is there a reason why the package does not recognise 0/1/2? (homozygous for reference allele, heterozygous and homozygous for the alternate allele)?

Thanks!

choishingwan commented 4 years ago

Hi, If you see the all samples removed due to missingness in covariate file, you should check if the combination of the missingness in your covariates are causing the problem e.g. a covariate structure like sample_1 1 NA 0 sample_2 NA 1 0 sample_3 1 1 NA will cause all three samples to be removed

In addition, you can check the log of PRSice which will tell you if one particular covariate are responsible for the removal (e.g. forgot to define a factor covariate)

Could you elaborate more about recognizing 0/1/2>

SaraBandres commented 4 years ago

Yes, but my question is. What do I do if i don't have the covariate information for all the samples? I cannot use them at all in the model?

choishingwan commented 4 years ago

You will need to do some kind of imputation of the covariates before you can use all of them. This is just like when you are trying to do a regression with a lot of missing data

On Sat, 14 Dec 2019 at 2:36 PM, SaraBandres notifications@github.com wrote:

Yes, but my question is. What do I do if i don't have the covariate information for all the samples? I cannot use them at all in the model?

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stale[bot] commented 4 years ago

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