Difference between revisions of "RAREFY DOCUMENTATION"
From Genome Analysis Wiki
Jump to navigationJump to searchShuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
||
| Line 1: | Line 1: | ||
==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 22: | Line 22: | ||
==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 --traitDecreasing --traitDecreasing --prefix your.output.prefix | ||
| + | *To analyze families using MCMC method in 3 chains and 50000000 iterations: | ||
| + | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix | ||
| + | *To inverse Normalize the phenotype before analysis: | ||
| + | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --inverseNormal --prefix your.output.prefix | ||
| + | *To analyze only a subset of families in the sample: | ||
| + | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix | ||
| + | *To analyze only one family: | ||
| + | rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famID fam123 --prefix your.output.prefix | ||
Revision as of 19:04, 16 February 2015
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.
INPUT FILE 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.
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 []
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 --traitDecreasing --traitDecreasing --prefix your.output.prefix
- To analyze families using MCMC method in 3 chains and 50000000 iterations:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix
- To inverse Normalize the phenotype before analysis:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --inverseNormal --prefix your.output.prefix
- To analyze only a subset of families in the sample:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix
- To analyze only one family:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famID fam123 --prefix your.output.prefix
