What arguments should I pass to pass to run in exhaustive mode?

[sahwa]

Hi @WansonChoi,

Thanks for your piece of software.

I'd like to run the omnibus test in exhaustive mode. However, it's not clear to me what needs passing to the --exhaustive argument on the command line. Trying --exhaustive True or any other string after results in the error HLAassoc: error: unrecognized arguments: True and leaving the argument empty --exhaustive results in HLAassoc/src/run_omnibus_test_LOGISTIC.R: error: argument --exhaustive: expected one argument Execution halted in the log file.

What should I pass to this argument to run in exhaustive mode?

My overall commmand is like this

python \
        -m HLAassoc OMNIBUS_LOGISTIC \
        --phased chr6.dose.G_group.filtered.${RC}.bgl.gz \
        --bim chr6.dose.G_group.filtered.${RC}.bim \
        --fam chr6.dose.G_group.filtered.${RC}.fam \
        --out output/hep_b_python_HLA_snps_logistic.${RC}.exhaustive \
        --pheno hep_b_phenos_omnibus.txt  \
        --covars hep_b_covars_omnibus.${RC}.txt \
        --exhaustive True \
        --aa-only \
        --maf-threshold 0

Thanks,

Sam

[yluo86]

sorry for the lack of documentation on this the --exhaustive argument should follow by the gene that one wants to perform exhaustive search on. You can also provide further argument to further restrict the search. For example, the following arguments will allow you three amino acid exhaustive search in HLA-B while fixing position 67 and 97

--exhaustive B --exhaustive-aa-pos 67 97 --exhaustive-min-aa 3 --exhaustive-max-aa 3 --exhaustive-no-filter