help documentation

[calebglossrex]

Hi there,

I was wondering if there would be more of an expansion of the help documentation in the future. In particular, I'm wondering how the covariance matrix should be coded/structured and am having trouble figuring that out based on the information available. I have played with some of the sample data sets, but still am uncertain as to how to proceed.

Thanks so much.

[variani]

Hi,

Adding more documentation is not a priority right now. The preprint together with supplementary material and vignette is the best place to see code examples and explanations.

My hope is that lme4 users can easily run lme4qtl.

Let me know if you have any specific question.

Best, Andrey

[calebglossrex]

Hi Andrey,

Thank you so much for the prompt reply. My apologies for the delayed response, I must have missed this email.

I was trying to run the relmatLmer function using a matrix I coded for the relmat = list(myID = myMatrix)) argument. Specifically, I'm working with family data and the covariance matrix I coded is a symmetric matrix of the genetic relatedness between the subjects in the sample (MZ twins = 1, DZ twins and full siblings = 0.5, half-siblings = 0.25, and unrelated subjects = 0). However, when I enter this matrix in lieu of myMatrix, the error is the folowing

I'm certain my matrix is symmetric so that error doesn't quite make sense.

I also noticed that the matrix (kin2) you use in your toy data set (dat40) ​is a Sparse matrix, so I made my matrix a sparse matrix to see if that would help. Still no dice, same error.

I'm wondering what you might suggest.

Thanks.

Best, Briana

On Fri, Dec 1, 2017 at 4:34 PM, Andrey Ziyatdinov notifications@github.com wrote:

Hi,

Adding more documentation is not a priority right now. The preprint https://www.biorxiv.org/content/early/2017/08/31/139816 together with supplementary material and vignette https://github.com/variani/lme4qtl/blob/master/vignettes/pedigreemm.Rmd is the best place to see code examples and explanations.

My hope is that lme4 users can easily run lme4qtl.

Let me know if you have any specific question.

Best, Andrey

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/variani/lme4qtl/issues/4#issuecomment-348620236, or mute the thread https://github.com/notifications/unsubscribe-auth/AbXU_yBMwtqLYCHaEEnhFOm97x31Lz5Eks5s8HDlgaJpZM4Qyvcf .

[variani]

Hi Briana,

I can't see the error messages in your previous post. Could you send this info. again? Also, it would be helpful to have a reproducible example, e.g., on simulated data.

Based on description of your data (the kinship matrix), I don't see any reason why relmatLmer would not work.

Best, Andrey