Difference between revisions of "RAREFY COMMAND"
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| + | == Useful Wiki Pages == | ||
| + | * The [[RAREFY | '''RAREFY Home''']] | ||
| + | * The [[RAREFY_DOC | '''RAREFY Documentation''']] | ||
| + | * The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']] | ||
| + | * The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']] | ||
| + | * The [[RAREFY_FAQ | '''FAQ''']] | ||
| + | |||
| + | ==RAREFY COMMANDS== | ||
Options: | Options: | ||
Input Files : --ped [], --dat [] | Input Files : --ped [], --dat [] | ||
| Line 9: | Line 17: | ||
==Input Files== | ==Input Files== | ||
| − | ===--ped=== | + | ===--ped [string]=== |
| − | followed by the file name of your[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file. | + | followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file. |
| − | ===--dat=== | + | ===--dat [string]=== |
followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format DAT] file. | followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format DAT] file. | ||
==Methods== | ==Methods== | ||
| − | ===--MCMC=== | + | ===--MCMC [on|off]=== |
| − | + | default is '''off''', but will be automatically turned on for families larger than 25 individuals. | |
| − | ===--traitIncreasing=== | + | |
| − | + | ===--traitIncreasing [on|off]=== | |
| − | ===--traitDecreasing=== | + | 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== | ==Trait== | ||
| − | ===--inverseNormal=== | + | ===--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=== | + | ===--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=== | + | ===--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== | ||
| + | ===--seed [int]=== | ||
| + | ===--chains [int]=== | ||
| + | The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains. | ||
| + | ===--iterations [int]=== | ||
| + | The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total. | ||
| + | |||
| + | ==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 to [[RAREFY_DOWNLOAD | '''COMPILE''']] for more information. | ||
| + | |||
| + | ===--prefix [string]=== | ||
| + | This option allows users to customize the output prefix generated by RAREFY. | ||
Latest revision as of 05:09, 17 February 2015
Useful Wiki Pages
- The RAREFY Home
- The RAREFY Documentation
- The RAREFY Tutorial
- The RAREFY Download Page
- The FAQ
RAREFY COMMANDS
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 your MERLIN 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 [int]
--chains [int]
The default is 3. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains.
--iterations [int]
The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total.
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 to COMPILE for more information.
--prefix [string]
This option allows users to customize the output prefix generated by RAREFY.
