Difference between revisions of "RAREFY COMMAND"

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(Methods)
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==Methods==
 
==Methods==
===--MCMC [ON|OFF]===
+
===--MCMC [on|off]===
default is '''OFF''', but will be automatically turned on for families larger than 25 individuals.
+
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.
  
===--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.

MCMC

--seed [double]

--chains [int]

--iterations [int]