Difference between revisions of "RAREFY COMMAND"
Shuang Feng (talk | contribs) (→Trait) |
Shuang Feng (talk | contribs) (→MCMC) |
||
| Line 43: | Line 43: | ||
===--chains [int]=== | ===--chains [int]=== | ||
===--iterations [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. | ||
| + | ===--prefix [string]=== | ||
| + | This option allows users to customize the output prefix generated by RAREFY. | ||
Revision as of 19:59, 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.
--prefix [string]
This option allows users to customize the output prefix generated by RAREFY.
