JWAS Module



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using JWAS



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?JWAS









    



search: JWAS







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JWAS.jl

JWAS.jl is an open-source software tool written in Julia for Bayesian multiple regression methods applied to genome-wide association studies and genomic prediction.

homepage: QTL.rocks
Installation: at the Julia REPL, Pkg.add("JWAS")
Documentaion: available here

Structure of JWAS Module
JWAS.jl

├──────── PedModule.jl

├──────── ST.jl
           ├── build_model
           ├── set_covariate
           ├── set_random
           ├── get_pedigree
           ├── add_markers
           ├── outputMCMCsamples
           ├── showMME
           ├── solve
           └── runMCMC

├──────── MT.jl
           ├── MT.build_model
           ├── MT.set_covariate
           ├── MT.set_random
           ├── MT.get_pedigree
           ├── MT.add_markers
           ├── MT.showMME
           ├── MT.solve
           └── MT.runMCMC

├──────── misc.jl
           ├── get_breeding_values
           ├── get_additive_genetic_variances
           ├── get_heritability
           ├── get_correlations
           └── report


├──────── Datasets.jl
Help

Show this README file in REPL or notebook using ?JWAS
For help on a specific function above, type ? followed by its name, e.g. ?runMCMC and press enter.
Run Pkg.checkout("JWAS") to get the newest unofficial JWAS. Run Pkg.free("JWAS") to go back to the offical one.



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using JWAS
#using JWAS.PedModule,JWAS.misc



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?add_markers









    



search: add_markers







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add_markers(mme::MME,file,G;separator=' ',header=true,G_is_marker_variance=false,df=4)

Get marker informtion from a genotype file (same order as the phenotype file).
G defaults to the marker effect  variance with degree of freedom df=4.0.
File format:


Animal,marker1,marker2,marker3,marker4,marker5
S1,1,0,1,1,1
D1,2,0,2,2,1
O1,1,2,0,1,0
O3,0,0,2,1,1