logicFS: Identification of SNP Interactions

Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.

Author
Holger Schwender
Date of publication
None
Maintainer
Holger Schwender <holger.schw@gmx.de>
License
LGPL (>= 2)
Version
1.44.0

View on Bioconductor

Man pages

data.logicfs
Example Data of logicFS
getMatEval
Evaluate Prime Implicants
logic.bagging
Bagged Logic Regression
logicFS
Feature Selection with Logic Regression
logicFS-internal
Internal logicFS functions
logic.oob
Prime Implicants
logic.pimp
Prime Implicants
make.snp.dummy
SNPs to Dummy Variables
mlogreg
Multinomial Logic Regression
plot.logicFS
Variable Importance Plot
predict.logicBagg
Predict Method for logicBagg objects
predict.mlogreg
Predict Method for mlogreg Objects
print.logicFS
Print a logicFS object
vim.approxPval
Approximate P-Value Based Importance Measure
vim.chisq
ChiSquare Based Importance
vim.ebam
EBAM Based Importance
vim.individual
VIM for Inputs
vim.logicFS
Importance Measures
vim.norm
Standardized and Sign-Permutation Based Importance Measure
vim.permSet
Permutation Based Importance Measures
vim.set
VIM for SNPs and Sets of Variables

Files in this package

logicFS/DESCRIPTION
logicFS/NAMESPACE
logicFS/R
logicFS/R/check.listprimes.R
logicFS/R/check.mat.imp.R
logicFS/R/check4NullModels.R
logicFS/R/checkDataCl.R
logicFS/R/checkNewTree.R
logicFS/R/checkSet.R
logicFS/R/compLarger.R
logicFS/R/compMatImpIndividual1.R
logicFS/R/compMatImpIndividual3.R
logicFS/R/compMatImpSet1.R
logicFS/R/compMatImpSet3.R
logicFS/R/compMatProbMLR.R
logicFS/R/contr.none.R
logicFS/R/contr.snps.R
logicFS/R/correctMultinomial.R
logicFS/R/correctPreds1.R
logicFS/R/correctPredsPermute1.R
logicFS/R/correctPredsPermute3.R
logicFS/R/correctPredsRemove1.R
logicFS/R/correctPredsRemove3.R
logicFS/R/correctQuantitative.R
logicFS/R/correctSetPermute1.R
logicFS/R/correctSetPermute3.R
logicFS/R/correctSetRemove1.R
logicFS/R/correctSetRemove3.R
logicFS/R/getKnots.R
logicFS/R/getMatEval.R
logicFS/R/getNames.R
logicFS/R/getNewTree.R
logicFS/R/getTree.R
logicFS/R/getVarInTree.R
logicFS/R/getXy.R
logicFS/R/getXyPred.R
logicFS/R/getY.R
logicFS/R/logic.bagging.R
logicFS/R/logic.oob.R
logicFS/R/logic.pimp.R
logicFS/R/logicFS.R
logicFS/R/make.snp.dummy.R
logicFS/R/makeContrastList.R
logicFS/R/mlogreg.R
logicFS/R/modelMat.R
logicFS/R/oobMLR.R
logicFS/R/plot.logicBagg.R
logicFS/R/plot.logicFS.R
logicFS/R/predict.logicBagg.R
logicFS/R/predict.logregmodel.R
logicFS/R/predict.mlogreg.R
logicFS/R/predictMLB.R
logicFS/R/print.logicBagg.R
logicFS/R/print.logicFS.R
logicFS/R/print.mlogreg.R
logicFS/R/standardizeMatImp.R
logicFS/R/vim.MLR.R
logicFS/R/vim.approxPval.R
logicFS/R/vim.chisq.R
logicFS/R/vim.ebam.R
logicFS/R/vim.individual.R
logicFS/R/vim.lm.R
logicFS/R/vim.logicFS.R
logicFS/R/vim.multiple.R
logicFS/R/vim.multiple.oneprime.R
logicFS/R/vim.norm.R
logicFS/R/vim.permInput.R
logicFS/R/vim.permSet.R
logicFS/R/vim.set.R
logicFS/R/vim.signperm.R
logicFS/R/vim.single.R
logicFS/R/zzz.R
logicFS/build
logicFS/build/vignette.rds
logicFS/data
logicFS/data/data.logicfs.RData
logicFS/inst
logicFS/inst/doc
logicFS/inst/doc/logicFS.R
logicFS/inst/doc/logicFS.Rnw
logicFS/inst/doc/logicFS.pdf
logicFS/man
logicFS/man/data.logicfs.Rd
logicFS/man/getMatEval.Rd
logicFS/man/logic.bagging.Rd
logicFS/man/logic.oob.Rd
logicFS/man/logic.pimp.Rd
logicFS/man/logicFS-internal.Rd
logicFS/man/logicFS.Rd
logicFS/man/make.snp.dummy.Rd
logicFS/man/mlogreg.Rd
logicFS/man/plot.logicFS.Rd
logicFS/man/predict.logicBagg.Rd
logicFS/man/predict.mlogreg.Rd
logicFS/man/print.logicFS.Rd
logicFS/man/vim.approxPval.Rd
logicFS/man/vim.chisq.Rd
logicFS/man/vim.ebam.Rd
logicFS/man/vim.individual.Rd
logicFS/man/vim.logicFS.Rd
logicFS/man/vim.norm.Rd
logicFS/man/vim.permSet.Rd
logicFS/man/vim.set.Rd
logicFS/vignettes
logicFS/vignettes/logicFS.Rnw
logicFS/vignettes/logicfs.png
logicFS/vignettes/logicfs.ps