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logicFS specifications

Information


Unique identifier OMICS_10095
Name logicFS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.50.0
Stability Stable
Requirements
genefilter, siggenes, LogicReg, mcbiopi
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Ingo Ruczinski

Publication for logicFS

logicFS citations

 (6)
library_books

Big Data Analysis Using Modern Statistical and Machine Learning Methods in Medicine

2014
PMCID: 4076480
PMID: 24987556
DOI: 10.5213/inj.2014.18.2.50

[…] quantified by the proportion of models in which the SNP combinations appear. Interactions that are only significant in small subgroups of the population thus have the potential to be overlooked. The LogicFS [] approach to logic regression uses sampling to address this issue. Another advantage of the LogicFS approach is that, unlike MCMC logic regression, it uses two unique measures that allow for […]

library_books

Identifying Interacting Genetic Variations by Fish Swarm Logic Regression

2013
Biomed Res Int
PMCID: 3747618
PMID: 23984382
DOI: 10.1155/2013/574735

[…] ~jiw09003/.Three existing LR-based approaches are compared, which are Monte Carlo logic regression (MCLR) [], full Bayesian logic regression (FBLR) [], and the SNP(s) importance measurement approach (LogicFS) []. The software package attached to MCLR is LogicReg, the software package for FBLR is SCRIME, and for the SNP importance measurement approach, LogicFS is the name of the software package. W […]

call_split

LBoost: A Boosting Algorithm with Application for Epistasis Discovery

2012
PLoS One
PMCID: 3493573
PMID: 23144812
DOI: 10.1371/journal.pone.0047281
call_split See protocol

[…] ng in tree , such that is an -dimensional column vector of 0 s and 1 s corresponding to the PI's value for the observations. We extract PIs from using the prime.implicant function available in the logicFS package . Let denote the matrix of all PIs in with randomly permuted. Let MC.T denote the tree-specific misclassification rate for applied to . The permutation based variable importance me […]

call_split

The Impact of Phenocopy on the Genetic Analysis of Complex Traits

2010
PLoS One
PMCID: 2912380
PMID: 20686705
DOI: 10.1371/journal.pone.0011876
call_split See protocol

[…] ith logistic regression where performed according to Clayton as developed in the “DGCgenetics” package. Interaction analysis by using a logic regression approach was performed by using the R package “logicFS” by Schwender, according to the developer's specifications.The MDR analysis has been conducted by using the MDR java package (www.epistasis.org) and performing 5.000 random explorations in the […]

library_books

Supervised learning based tagSNP selection for genome wide disease classifications

2008
BMC Genomics
PMCID: 2386071
PMID: 18366619
DOI: 10.1186/1471-2164-9-S1-S6

[…] given classifiers (NMSC, NBC, SVM, UDC) under different feature selections (two SVRFA: MSW-MSC, MMW-MSC; three SRFA: NBC-MSC, NMSC-MSC, DENFIS-MSC; three popular approaches: SVMRFE, Logistic-Wald-t, LOGICFS) for the MICC data set and NARAC CHR18SNP, respectively. In Table , the testing accuracies of LOGICFS were obtained from the 31 SNPs in the MICC data set without environmental variables. Altho […]

library_books

Empirical Bayes analysis of single nucleotide polymorphisms

2008
BMC Bioinformatics
PMCID: 2335278
PMID: 18325106
DOI: 10.1186/1471-2105-9-144

[…] ly be used to detect interesting variables or interactions. The posterior probabilities estimated by EBAM can also be employed to quantify the importance of features found by other approaches such as logicFS [].Logic regression [] – which is employed as base learner in logicFS – is an adaptive regression and classification procedure that searches for Boolean combinations of binary variables associ […]

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logicFS institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

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