domrec: DOMinant / RECessive reencoder

domrec is a very simple reencoder of plink BED/BIM/FAM files to dominant, recessive, or dominance deviation, so those modes can be tested with complex GWAS models that otherwise don't support them (i.e. generalized mixed-effects models). This c++ project converts genotypes on the fly, using practically no memory even for very large files.

Compliation from source

This project depends on the standard c++ library only, and can be compiled as usual:

make

If successful, you can test that outputs are as expected by comparing to an internal R version (requires genio CRAN package) that is more straighforward code but consumes way more memory on larger files (it is tested on a toy dataset where this is not a concern). The test passed if there are no error messages:

make test

Under build/ there is a version already compiled under my own Linux computer, which may work with other Linux systems.

Usage

domrec requires these three arguments:

domrec <input_base> <output_base> <mode>

• <input_base> is the shared base name of the input plink .bed, .bim, and .fam files, all of which are required.
• <output_base> is the base name of the output file. .bed extension is automatically added, but .bim and .fam are not created (they are not modified by this reencoding, so they can simply be copied or linked from the input).
• <mode> must equal one of these three choices, which describes the transformation:
  • dom: dominant encoding (changes heterozygotes (x=1) to minor allele homozygotes (x=2 if effect allele was minor, x=0 otherwise))
  • rec: recessive encoding (changes heterozygotes (x=1) to major allele homozygotes (x=0 if effect allele was minor, x=2 otherwise))
  • dev: dominance deviation encoding (changes heterozygotes (x=1) to effect allele homozygotes (x=2) and effect allele homozygotes (x=2) to non-effect allele homozygotes (x=0))