Difference between revisions of "RAREFY COMMAND"

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(--MCMC)
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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===
+
===--traitIncreasing [ON|OFF]===
[ON|OFF]: default is '''OFF'''; can be used together with '''--traitDecreasing''' options or used alone.
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default is '''OFF'''; can be used together with '''--traitDecreasing''' options or used alone.
===--traitDecreasing===
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===--traitDecreasing [ON|OFF]===
[ON|OFF]: default is '''OFF'''; can be used together with '''--traitIncreasing''' options or used alone.
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default is '''OFF'''; can be used together with '''--traitIncreasing''' options or used alone.
 
==Trait==
 
==Trait==
===--inverseNormal===
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===--inverseNormal [ON|OFF]===
[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).  
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default is '''OFF'''; '''ON''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option).  
===--useCovariates===
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===--useCovariates [ON|OFF]===
[ON|OFF]: default is '''OFF'''; '''ON''' will adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file).  
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default is '''OFF'''; '''ON''' will adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file).  
===--traitName===
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===--traitName [string]===
[your.trait.name.in.string]: default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).
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default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).
  
 
==Parameters==
 
==Parameters==
===--maf===
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===--maf [double]===
[your.preferred.frequency.value]:default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.
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default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.
  
===--effect===
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===--effect [double]===
[your.preferred.effect.size]:default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.
+
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==
 
==MCMC==
===--seed===
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===--seed [double]===
===--chains===
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===--chains [int]===
===--iterations===
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===--iterations [int]===

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]