Difference between revisions of "RAREFY COMMAND"

From Genome Analysis Wiki
Jump to: navigation, search
(--effect)
(Parameters)
Line 36: Line 36:
 
===--effect===
 
===--effect===
 
[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.
 
[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.
 +
 +
==MCMC==
 +
===--seed===
 +
===--chains===
 +
===--iterations===

Revision as of 19:50, 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

followed by the file name of yourMERLIN format PED file.

--dat

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

[your.trait.name.in.string]: default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).

Parameters

--maf

[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.

--effect

[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.

MCMC

--seed

--chains

--iterations