Difference between revisions of "RAREFY COMMAND"

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(--cpus [int])
(--cpus [int])
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===--cpus [int]===
 
===--cpus [int]===
 
This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.
 
This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.
NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer [RAREFY_DOWNLOAD | '''COMPILE'''] for more information.
+
NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer [[RAREFY_DOWNLOAD | '''COMPILE''']] for more information.
  
 
===--prefix [string]===
 
===--prefix [string]===
 
This option allows users to customize the output prefix generated by RAREFY.
 
This option allows users to customize the output prefix generated by RAREFY.

Revision as of 20:00, 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]

Others

--famList [string]

This options allows analysis of only a subset of families listed in a file. However, all families included in PED/DAT file will be used to fit variance component model.

--famID [string]

This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.

--cpus [int]

This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used. NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer COMPILE for more information.

--prefix [string]

This option allows users to customize the output prefix generated by RAREFY.