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 [string]
followed by the file name of yourMERLIN format PED file.
--dat [string]
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 [string]
default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).
Parameters
--maf [double]
default is 0.001; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.
--effect [double]
default is 1 SD; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.
MCMC
--seed [double]
--chains [int]
--iterations [int]
Others
--famList [string]
This options allows analysis of only a subset of families listed in a file. However, all families included in PED/DAT file will be used to fit variance component model.
--famID [string]
This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.
--cpus [int]
This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used. NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer [RAREFY_DOWNLOAD | COMPILE] for more information.
--prefix [string]
This option allows users to customize the output prefix generated by RAREFY.