Difference between revisions of "RAREFY COMMAND"
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==Methods== | ==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. | ||
Revision as of 19:40, 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.
