Difference between revisions of "RAREFY COMMAND"
Shuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) (→Trait) |
||
Line 24: | Line 24: | ||
==Trait== | ==Trait== | ||
===--inverseNormal=== | ===--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=== | ===--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). |
Revision as of 19:45, 16 February 2015
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).