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RAREFY DOCUMENTATION

2,539 bytes added, 05:08, 17 February 2015
Useful Wiki Pages
== Useful Wiki Pages ==
 
* The [[RAREFY | '''RAREFY Home''']]
* The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']]
* The [[RAREFY_COMMAND | '''RAREFY Command Reference''']]
* The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']]
* The [[RAREFY_FAQ | '''FAQ''']]
 
==KEY FEATURES==
*'''RAREFY''' is a likelihood-based method to prioritize individuals in family samples and AND population samples.
*'''RAREFY''' takes account familial relatedness and allows adjusting covariates.
*'''RAREFY''' is able to handle large and complex pedigrees.
==DOWNLOAD & BUILD==Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables. ==INPUT FILE FORMAT==
*'''RAREFY''' takes [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED/DAT files] as input, no MAP file is needed.
*Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.
 
==OUTPUT FORMAT==
'''RAREFY''' generates output file with eight columns.
==SOFTWARE INTERFACE==
Options:
Input Files : --ped [], --dat []
Methods : --MCMC, --traitIncreasing, --traitDecreasing
Trait : --inverseNormal, --logTransform, --useCovariates, --traitName [] Parameters : --maf [1.0e-03], --effect [21.00]
MCMC : --seed, --chains [3], --iterations [50000000]
Other : --famList [], --famID [], --cpus [5], --prefix [] Please see [[RAREFY_COMMAND| '''RAREFY COMMAND REFERENCE''']] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES | '''EXAMPLES''']] for quick examples.
==EXAMPLES==
*To prioritize individuals likely to be carriers of trait-increasing rare variants:
rarefy --ped your.ped --dat your.dat --traitIncreasing --prefix your.output.prefix
*To prioritize individuals likely to be carriers of trait-decreasing rare variants:
rarefy --ped your.ped --dat your.dat --traitDecreasing --prefix your.output.prefix
*To prioritize individuals likely to be carriers of either trait-decreasing or trait-decreasing rare variants:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --prefix your.output.prefix
*To analyze families using MCMC method in 3 chains and 50000000 iterations:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix
*To inverse Normalize the phenotype before analysis:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --prefix your.output.prefix
*To inverse Normalize the phenotype and then adjust covariates saved in PED/DAT file before RAREFY analysis:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --useCovariates --prefix your.output.prefix
*To analyze only a subset of families in the sample:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix
NOTE: although only the subset of families will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.
*To analyze only one family:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famID fam123 --prefix your.output.prefix
NOTE: although only the family included in --famID will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.
*To analyze only one trait saved in your.ped and your.dat file:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --traitName LDL --prefix your.output.prefix
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