Package: logicFS 2.27.0

Holger Schwender

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.

Authors:Holger Schwender, Tobias Tietz

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logicFS.pdf |logicFS.html✨
logicFS/json (API)

# Install 'logicFS' in R:

install.packages('logicFS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

cl.logicfs - Example Data of logicFS
data.logicfs - Example Data of logicFS

On BioConductor:logicFS-2.25.0(bioc 3.20)logicFS-2.24.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

snp classification genetics

3.60 score 8 scripts 310 downloads 2 mentions 26 exports 5 dependencies

Last updated 23 days agofrom:235b3ea3f2. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:contr.none contr.snps getMatEval getXy logic.bagging logic.oob logic.pimp logicFS make.snp.dummy mlogreg survivalFS vim.approxPval vim.chisq vim.ebam vim.individual vim.input vim.logicFS vim.norm vim.permInput vim.permSet vim.permSNP vim.set vim.signperm vim.singleBoth vim.singleRemove vim.snp

Dependencies:lattice LogicReg Matrix mcbiopi survival

logicFS Manual

Rendered fromlogicFS.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2020-04-11
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example Data of logicFS	cl.logicfs data.logicfs
Evaluate Prime Implicants	getMatEval
Bagged Logic Regression	logic.bagging logic.bagging.default logic.bagging.formula print.logicBagg
Prime Implicants	logic.oob
Prime Implicants	logic.pimp
Feature Selection with Logic Regression	logicFS logicFS.default logicFS.formula logicFS.logicBagg
SNPs to Dummy Variables	make.snp.dummy
Multinomial Logic Regression	mlogreg mlogreg.default mlogreg.formula print.mlogreg
Variable Importance Plot	plot.logicBagg plot.logicFS
Survival and Cumulative Hazard Function Plot	plot.predict.survivalFS print.predict.survivalFS
Predict Method for logicBagg objects	predict.logicBagg
Predict Method for mlogreg Objects	predict.mlogreg
Print a logicFS object	print.logicFS
Logic Feature Selection for Survival Data	survivalFS survivalFS.default survivalFS.formula survivalFS.logicBagg
Approximate P-Value Based Importance Measure	vim.approxPval
ChiSquare Based Importance	vim.chisq
EBAM Based Importance	vim.ebam
VIM for Inputs	vim.individual vim.input
Importance Measures	vim.logicFS
Standardized and Sign-Permutation Based Importance Measure	vim.norm vim.signperm
Permutation Based Importance Measures	vim.permInput vim.permSet vim.permSNP
VIM for SNPs and Sets of Variables	vim.set vim.snp