I know that we can impute missing genotypes in GWAS studies by inferring from the Hapmap or 1000-genomes genotypes. However, candidate gene studies can not use this method. Can I use the general imputation methods (e.g Amelia or other general imputation packages in R) to impute five datasets and then combine them in the analysis? Thank you.
Could you share more details about your design? Otherwise it is not easy to comment/help. Basically you can impute whatever you like if you have a panel (for instance here a set of individuals sequenced for you candidate gene.
Moreover, Amelia is not imputation program, this is a program that uses imputed (and analyzed) genotypes (SNPTEST format as far as I remember).
Again, if you describe the design, we could help