Hi Dr. Bates,
Thank you very much for your help. I was able to code the lmm to run across
the matrix with your helpful suggestions.
All the best,
Christina
On Friday, March 18, 2016 at 11:49:37 AM UTC-4, Christina Castellani wrote:
>
> I apologize for the beginner nature of my question but I am not
> understanding the file structure in Julia.
>
> I am wanting to run lmm on a very large file (470000x2000), I would like
> to run one lmm on each of the 470000 observations.
>
> I have loaded in my matrix and my covariates to Julia using the following
> code:
> betas = readtable("betas.txt", separator='\t')
>
> covarsInput=readtable("covarsInputJulia.csv")
>
> covarsInput[:CNValues]=PooledDataArray(covarsInput[:CNValues])
> covarsInput[:Age]=PooledDataArray(covarsInput[:Age])
> covarsInput[:Sex]=PooledDataArray(covarsInput[:Sex])
> covarsInput[:ChipID]=PooledDataArray(covarsInput[:ChipID])
>
>
> I am then running an lmm, in this fashion:
> m=fit!(lmm(betas~CNValues+Age+Sex+(1|ChipID1911),covarsInput))
>
> This will not run because covarsInput is the dataframe being specified and
> betas is not in covarsInput. I have no idea how to remedy this?
> So a) how do I get all my files in the same "dataframe" even if one is a
> large matrix, and
> b) how do I get the lmm to run on each probe in betas
>
> Any help you can provide is greatly appreciated, I am very new to this and
> pretty confused!
>
> Thank you!
>
