Post by dgurdasani on Sept 23, 2014 15:42:46 GMT
Hi,
I'm trying to analyse GWAS data on 34 traits for 5000 related individuals on the X chromosome- I've managed to check which model (full dosage compensation vs no dosage compensation) fits well for each phenotype, by checking which has the maximum likelihood. Based on this, I'd like to carry out mixed model analysis specifying different models on the X chromsome- this would require GCTA to code the X chromosome as 0,1 in males and 0,1,2 in females for no dosage compensation, and 0,2 in males and 0,1,2 in females for full dosage compensation. Is there a way I can specify this in GCTA, so it carries out model aware analysis?
Also, would it be best to include both the autosomal and relevant X chromosomal GRM in such an analysis?
Thanks for your help.
Best wishes,
Deepti
I'm trying to analyse GWAS data on 34 traits for 5000 related individuals on the X chromosome- I've managed to check which model (full dosage compensation vs no dosage compensation) fits well for each phenotype, by checking which has the maximum likelihood. Based on this, I'd like to carry out mixed model analysis specifying different models on the X chromsome- this would require GCTA to code the X chromosome as 0,1 in males and 0,1,2 in females for no dosage compensation, and 0,2 in males and 0,1,2 in females for full dosage compensation. Is there a way I can specify this in GCTA, so it carries out model aware analysis?
Also, would it be best to include both the autosomal and relevant X chromosomal GRM in such an analysis?
Thanks for your help.
Best wishes,
Deepti
