Difference between revisions of "RAREFY COMMAND"
Shuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
||
Line 16: | Line 16: | ||
==Methods== | ==Methods== | ||
− | ===--MCMC [ | + | ===--MCMC [on|off]=== |
− | default is ''' | + | 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== | ==Trait== | ||
===--inverseNormal [ON|OFF]=== | ===--inverseNormal [ON|OFF]=== |
Revision as of 19:53, 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.