RAREFY DOCUMENTATION: Difference between revisions
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== 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== | ==KEY FEATURES== | ||
*'''RAREFY''' is a likelihood-based method to prioritize individuals in family | *'''RAREFY''' is a likelihood-based method to prioritize individuals in family AND population samples. | ||
*'''RAREFY''' takes account familial relatedness and allows adjusting covariates. | *'''RAREFY''' takes account familial relatedness and allows adjusting covariates. | ||
| Line 7: | Line 15: | ||
*'''RAREFY''' is able to handle large and complex pedigrees. | *'''RAREFY''' is able to handle large and complex pedigrees. | ||
==INPUT | ==DOWNLOAD & BUILD== | ||
Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables. | |||
==INPUT 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. | *'''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== | ==SOFTWARE INTERFACE== | ||
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 [] | |||
Please see [[RAREFY_COMMAND| '''RAREFY COMMAND REFERENCE''']] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES | '''EXAMPLES''']] for quick examples. | |||
==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 | |||
Latest revision as of 05:08, 17 February 2015
Useful Wiki Pages
- The RAREFY Home
- The RAREFY Download Page
- The RAREFY Command Reference
- The RAREFY Tutorial
- The FAQ
KEY FEATURES
- RAREFY is a likelihood-based method to prioritize individuals in family 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 DOWNLOAD PAGE for source code and executables.
INPUT FORMAT
- RAREFY takes 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, --useCovariates, --traitName []
Parameters : --maf [1.0e-03], --effect [1.00]
MCMC : --seed, --chains [3], --iterations [50000000]
Other : --famList [], --famID [], --cpus [5], --prefix []
Please see RAREFY COMMAND REFERENCE for detailed description of usage, and 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
