RAREFY COMMAND: Difference between revisions
Shuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
||
| Line 25: | Line 25: | ||
==Trait== | ==Trait== | ||
===--inverseNormal [ | ===--inverseNormal [on|off]=== | ||
default is ''' | 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 ''' | default is '''off'''; '''on''' will adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file). | ||
===--traitName [string]=== | ===--traitName [string]=== | ||
default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file). | default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file). | ||
Revision as of 19:54, 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 [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.
