RAREFY COMMAND: Difference between revisions
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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. | ||
===--traitDecreasing | ===--traitDecreasing [ON|OFF]=== | ||
[ON|OFF] | default is '''OFF'''; can be used together with '''--traitIncreasing''' options or used alone. | ||
==Trait== | ==Trait== | ||
===--inverseNormal | ===--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). | ||
===--useCovariates | ===--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). | ||
===--traitName=== | ===--traitName [string]=== | ||
default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file). | |||
==Parameters== | ==Parameters== | ||
===--maf=== | ===--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=== | ===--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== | ==MCMC== | ||
===--seed=== | ===--seed [double]=== | ||
===--chains=== | ===--chains [int]=== | ||
===--iterations=== | ===--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.
