Assigns a new phenotype status to individuals by looking at family members, for use in Genome Wide Association Studies by proxy (GWAX).
assign_GWAX_phenotype(pheno_file, output_file = pheno_file, sibs)
| pheno_file | path to file with information on phenotype status, i.e. the file "phenotypes.txt" generated by simulation functions. |
|---|---|
| output_file | path of output file, including file extension ".txt". |
| sibs | optional: specify number of siblings to use for proxy. Defaults to using all of an individual's siblings. |
Does not return anything, but writes output_file to disk,
where the GWAX phenotype column is appended to the end of pheno_file.
An individual, who is registered as a control, will be assigned case, if any
of its family members are cases. Otherwise the phenotype status is the
same.
Note: The `sibs` argument can be used for limiting how many siblings
are taken into consideration when creating the new phenotype This allows for
different analyses with the same simulation, see for instance
vignette("geneference").