Error in calculateDiffMeth for covariates with NAs

[TYRANISTAR]

Hello,

I've been using MethylKit to analyse RRBS data from human samples and I noticed that when I introduce covariates with one or more NAs in them (e.g. if one of my covariates is age and I don't know the age of one of my samples) it crashes the calculateDiffMeth() function. The error I get is the following:

Error in p.adjust(pvals, method = method, n) : n >= lp is not TRUE

Is there a way around it? Do I always have to use covariate variables without any NAs in them?

Thank you in advance.

[al2na]

I don't think we can deal with that case. Covariates shouldn't have missing data probably if I'm not mistaken.

On Fri, Sep 17, 2021 at 11:23 PM TYRANISTAR @.***> wrote:

Hello,

I've been using MethylKit to analyse RRBS data from human samples and I noticed that when I introduce covariates with one or more NAs in them (e.g. if one of my covariates is age and I don't know the age of one of my samples) it crashes the calculateDiffMeth() function. The error I get is the following:

Error in p.adjust(pvals, method = method, n) : n >= lp is not TRUE

Is there a way around it? Do I always have to use covariate variables without any NAs in them?

Thank you in advance.

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