RAREFY COMMAND
Options:
Input Files : --ped [], --dat []
Methods : --MCMC, --traitIncreasing, --traitDecreasing
Trait : --inverseNormal, --useCovariates, --traitName []
Parameters : --maf [1.0e-03], --effect [1.00]
MCMC : --seed, --chains [3], --iterations [50000000]
Other : --famList [], --famID [], --cpus [5], --prefix []
Input Files
--ped
followed by the file name of yourMERLIN format PED file.
--dat
followed by the file name of your MERLIN format DAT file.
Methods
--MCMC
[ON|OFF]: default is OFF, but will be automatically turned on for families larger than 25 individuals.
--traitIncreasing
[ON|OFF]: default is OFF; can be used together with --traitDecreasing options or used alone.
--traitDecreasing
[ON|OFF]: default is OFF; can be used together with --traitIncreasing options or used alone.
Trait
--inverseNormal
[ON|OFF]: default is OFF; ON will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option).
--useCovariates
[ON|OFF]: default is OFF; ON will adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file).
--traitName
[your.trait.name.in.string]: default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).
Parameters
--maf
[your.preferred.frequency.value]:default is 0.001; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.
--effect
[your.preferred.effect.size]:default is 1 standard deviation; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.
