Dominance effect SNP estimate

Question

[joao_gabrielzp]

Hi everyone!

I'm trying to estimate the additive and dominance SNP effects in order to obtain the allelic substitution effect.

I'm actualy having two problems, one with R and another with PLINK.

The R one: I'm regressing my phenotypes over my SNPs using both linear regression and mixed modelling. For the additive effects I had no issues (code 0,1,2), but for the dominant one (code 0,1,1) I'm having some troubles. When I coded my SNPs to do the dominant regression, some loci ended up with just the code "1", which obviously caused problems in my analysis, since, in this case, it is only one sampled level.

So, my question is, what is the right approach in this case? Should I exclude this loci? or maybe do something else?

The PLINK one: I've been told that --model can do this for me, and estimate both additive and dominant effects:

I'm using plink --ped mydata.txt --map mymapdata.map --allow-no-sex --pheno myphenodata.txt --out model

I'm getting this error: Error: --model requires a case/control phenotype. I' ve read about it in the PLINK page and still don't know what to do, can you guys help me?

Thanks in advance!!

Answer 1

[chrchang523]

1. Yes, there is no point in trying to perform dominance analysis when every single genotype has at least one copy of the allele; you have zero information for that.
2. Replace --model with "--linear genotypic" in your PLINK command to perform this analysis for a quantitative phenotype.

[joao_gabrielzp]

Thanks a lot for your answer!

1. That was what I was thinking, but the fact that I can analyze a certain SNP when the code is additive and not when it is dominant, kinda made me wonder if there was some approach to something like this that I was unware of.

2.I'm gonna try that, thanks!

[joao_gabrielzp]

Hi chrchang523!

1. Some of my loci got NA values for the dominance effect, since I excluded them like you told me to. But this caused some of my allelic substituion effects to also have NA values for some of my loci of interest (ASE = a+d(q-p)). Since I'm trying to estimate the heritability for these SNPs, this results in a NA heritability. What should I do in this case?

2. Using PLINK I get some NA's, which I supposed it's normal, but some of them are appearing for the loci I'm interested.too.

Thanks!!