GeneticSubsetter: Identify Favorable Subsets of Germplasm Collections

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Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.

Author
Ryan C. Graebner and Alfonso Cuesta-Marcos
Date of publication
2016-10-25 23:03:53
Maintainer
Ryan C. Graebner <ryan.graebner@gmail.com>
License
GPL (>= 2)
Version
0.8

View on CRAN

Man pages

CoreSetOptimizer
Subset Optimization
CoreSetter
Genotype Subsetting
CoreSetterCombined
Genotype Subsetting-Alternative Method
CoreSetterPoly
Genotype Subsetting for Autopolyploids and Polymorphic...
GeneticSubsetter
Genetic Subsetter
genotypes
Sample Barley Genotypes
genotypes.poly
Sample Barley Genotypes
HET
Heterozygosity Calculator
Mat
Kinship Matrix Creator
MTK
MTK calculator
MtkCalc
MTK calculator (Depreciated)
PicCalc
PIC Calculator (Depreciated)
SubsetterMTK
Genotype Subsetting with PIC - Method One (Depreciated)
SubsetterPIC
Genotype Subsetting with PIC - Method One (Depreciated)

Files in this package

GeneticSubsetter
GeneticSubsetter/inst
GeneticSubsetter/inst/doc
GeneticSubsetter/inst/doc/GeneticSubsetterUsersGuide.R
GeneticSubsetter/inst/doc/GeneticSubsetterUsersGuide.html
GeneticSubsetter/inst/doc/GeneticSubsetterUsersGuide.Rmd
GeneticSubsetter/NAMESPACE
GeneticSubsetter/data
GeneticSubsetter/data/genotypes.rda
GeneticSubsetter/R
GeneticSubsetter/R/CoreSetterPoly.R
GeneticSubsetter/R/SubsetterMTK.R
GeneticSubsetter/R/CoreSetOptimizer.R
GeneticSubsetter/R/CoreSetter.R
GeneticSubsetter/R/MtkCalc.R
GeneticSubsetter/R/PicCalc.R
GeneticSubsetter/R/MTK.R
GeneticSubsetter/R/HET.R
GeneticSubsetter/R/CoreSetterCombined.R
GeneticSubsetter/R/SubsetterPIC.R
GeneticSubsetter/R/Mat.R
GeneticSubsetter/vignettes
GeneticSubsetter/vignettes/GeneticSubsetterUsersGuide.Rmd
GeneticSubsetter/MD5
GeneticSubsetter/build
GeneticSubsetter/build/vignette.rds
GeneticSubsetter/DESCRIPTION
GeneticSubsetter/man
GeneticSubsetter/man/SubsetterMTK.Rd
GeneticSubsetter/man/PicCalc.Rd
GeneticSubsetter/man/HET.Rd
GeneticSubsetter/man/CoreSetOptimizer.Rd
GeneticSubsetter/man/Mat.Rd
GeneticSubsetter/man/SubsetterPIC.Rd
GeneticSubsetter/man/genotypes.Rd
GeneticSubsetter/man/MTK.Rd
GeneticSubsetter/man/GeneticSubsetter.Rd
GeneticSubsetter/man/CoreSetter.Rd
GeneticSubsetter/man/CoreSetterPoly.Rd
GeneticSubsetter/man/MtkCalc.Rd
GeneticSubsetter/man/genotypes.poly.Rd
GeneticSubsetter/man/CoreSetterCombined.Rd