OmicsMarkeR: Classification and Feature Selection for 'Omics' Datasets

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Tools for classification and feature selection for 'omics' level datasets. It is a tool to provide multiple multivariate classification and feature selection techniques complete with multiple stability metrics and aggregation techniques. It is primarily designed for analysis of metabolomics datasets but potentially extendable to proteomics and transcriptomics applications.

Author
Charles E. Determan Jr. <cdetermanjr@gmail.com>
Date of publication
None
Maintainer
Charles E. Determan Jr. <cdetermanjr@gmail.com>
License
GPL-3
Version
1.6.0
URLs

View on Bioconductor

Man pages

aggregation
Feature Aggregation
bagging.wrapper
Bagging Wrapper for Ensemble Features Selection
canberra
Canberra Distance
canberra_stability
Canberra Stability
CLA
Complete Linear Aggregation
create.corr.matrix
Correlated Multivariate Data Generator
create.discr.matrix
Discriminatory Multivariate Data Generator
create.random.matrix
Random Multivariate Data Generator
denovo.grid
Denovo Grid Generation
EE
Ensemble Exponential Aggregation
EM
Ensemble Mean Aggregation
ES
Ensemble Stability Aggregation
extract.args
Argument extractor
extract.features
Feature Extraction
feature.table
Feature Consistency Table
fit.only.model
Fit Models without Feature Selection
fs.ensembl.stability
Ensemble Classification & Feature Selection
fs.stability
Classification & Feature Selection
jaccard
Jaccard Index
kuncheva
Kuncheva's Index
modelList
Model List
modelTuner
Model Tuner
modelTuner_loo
Model Tuner for Leave-One-Out Cross-Validation
noise.matrix
Noise Matrix Generator
ochiai
Ochiai's Index
optimize.model
Model Optimization and Metrics
pairwise.model.stability
Pairwise Model Stability Metrics
pairwise.stability
Pairwise Stability Metrics
params
Model Parameters and Properties
perf.calc
Performance Statistics Calculations
performance.metrics
Performance Metrics of fs.stability or fs.ensembl.stability...
performance.stats
Performance Statistics (Internal for 'perf.calc')
perm.class
Monte Carlo Permutation of Model Performance
perm.features
Feature Selection via Monte Carlo Permutation
pof
Percentage of Overlapping Features
predicting
Model Group Prediction
prediction.metrics
Prediction Metric Calculations
predictNewClasses
Class Prediction
RPT
Robustness-Performance Trade-Off
sequester
Sequester Additional Parameters
sorensen
Dice-Sorensen's Index
spearman
Spearman Rank Correlation Coefficient
svmrfeFeatureRanking
SVM Recursive Feature Extraction (Binary)
svmrfeFeatureRankingForMulticlass
SVM Recursive Feature Extraction (Multiclass)
svm.weights
SVM Multiclass Weights Ranking
training
Model Training
tune.instructions
Model Optimization Instructions

Files in this package

OmicsMarkeR/.travis.yml
OmicsMarkeR/DESCRIPTION
OmicsMarkeR/NAMESPACE
OmicsMarkeR/R
OmicsMarkeR/R/aggregation.R
OmicsMarkeR/R/assert_functions.R
OmicsMarkeR/R/bagging.wrapper.v2.R
OmicsMarkeR/R/data.generation.R
OmicsMarkeR/R/denovo.grid.R.R
OmicsMarkeR/R/extract.args.R
OmicsMarkeR/R/extract.features.v2.R
OmicsMarkeR/R/feature.table.R
OmicsMarkeR/R/fit.only.model.R
OmicsMarkeR/R/fs.ensembl.stability.R
OmicsMarkeR/R/fs.stability.v2.R
OmicsMarkeR/R/misc.R
OmicsMarkeR/R/modelList.R
OmicsMarkeR/R/modelTuner.v2.R
OmicsMarkeR/R/modelTuner_loo.R
OmicsMarkeR/R/optimize.R
OmicsMarkeR/R/params.R
OmicsMarkeR/R/performance.R
OmicsMarkeR/R/performance.metrics.R
OmicsMarkeR/R/perm.class.R
OmicsMarkeR/R/perm.features.R
OmicsMarkeR/R/predictNewClasses.R
OmicsMarkeR/R/predicting.R
OmicsMarkeR/R/prediction.metrics.R
OmicsMarkeR/R/sequester.R
OmicsMarkeR/R/stability.R
OmicsMarkeR/R/svm.functions.R
OmicsMarkeR/R/training.R
OmicsMarkeR/R/tune.instructions.R
OmicsMarkeR/R/verify.R
OmicsMarkeR/README.md
OmicsMarkeR/appveyor.yml
OmicsMarkeR/build
OmicsMarkeR/build/vignette.rds
OmicsMarkeR/inst
OmicsMarkeR/inst/CITATION
OmicsMarkeR/inst/NEWS.Rd
OmicsMarkeR/inst/doc
OmicsMarkeR/inst/doc/OmicsMarkeR.R
OmicsMarkeR/inst/doc/OmicsMarkeR.Rnw
OmicsMarkeR/inst/doc/OmicsMarkeR.pdf
OmicsMarkeR/inst/examples
OmicsMarkeR/inst/examples/RPT.R
OmicsMarkeR/inst/examples/aggregation.R
OmicsMarkeR/inst/examples/canberra.R
OmicsMarkeR/inst/examples/data.generation.R
OmicsMarkeR/inst/examples/denovo.grid.R
OmicsMarkeR/inst/examples/feature.table.R
OmicsMarkeR/inst/examples/fit.only.model.R
OmicsMarkeR/inst/examples/fs.stability.R
OmicsMarkeR/inst/examples/jaccard.R
OmicsMarkeR/inst/examples/kuncheva.R
OmicsMarkeR/inst/examples/ochiai.R
OmicsMarkeR/inst/examples/pairwise.model.stability.R
OmicsMarkeR/inst/examples/pairwise.stability.R
OmicsMarkeR/inst/examples/params.R
OmicsMarkeR/inst/examples/performance.metrics.R
OmicsMarkeR/inst/examples/perm.class.R
OmicsMarkeR/inst/examples/perm.features.R
OmicsMarkeR/inst/examples/pof.R
OmicsMarkeR/inst/examples/predictNewClasses.R
OmicsMarkeR/inst/examples/sorensen.R
OmicsMarkeR/inst/examples/spearman.R
OmicsMarkeR/inst/examples/svmrfeFeatureRanking.R
OmicsMarkeR/inst/examples/svmrfeFeatureRankingForMulticlass.R
OmicsMarkeR/man
OmicsMarkeR/man/CLA.Rd
OmicsMarkeR/man/EE.Rd
OmicsMarkeR/man/EM.Rd
OmicsMarkeR/man/ES.Rd
OmicsMarkeR/man/RPT.Rd
OmicsMarkeR/man/aggregation.Rd
OmicsMarkeR/man/bagging.wrapper.Rd
OmicsMarkeR/man/canberra.Rd
OmicsMarkeR/man/canberra_stability.Rd
OmicsMarkeR/man/create.corr.matrix.Rd
OmicsMarkeR/man/create.discr.matrix.Rd
OmicsMarkeR/man/create.random.matrix.Rd
OmicsMarkeR/man/denovo.grid.Rd
OmicsMarkeR/man/extract.args.Rd
OmicsMarkeR/man/extract.features.Rd
OmicsMarkeR/man/feature.table.Rd
OmicsMarkeR/man/fit.only.model.Rd
OmicsMarkeR/man/fs.ensembl.stability.Rd
OmicsMarkeR/man/fs.stability.Rd
OmicsMarkeR/man/jaccard.Rd
OmicsMarkeR/man/kuncheva.Rd
OmicsMarkeR/man/modelList.Rd
OmicsMarkeR/man/modelTuner.Rd
OmicsMarkeR/man/modelTuner_loo.Rd
OmicsMarkeR/man/noise.matrix.Rd
OmicsMarkeR/man/ochiai.Rd
OmicsMarkeR/man/optimize.model.Rd
OmicsMarkeR/man/pairwise.model.stability.Rd
OmicsMarkeR/man/pairwise.stability.Rd
OmicsMarkeR/man/params.Rd
OmicsMarkeR/man/perf.calc.Rd
OmicsMarkeR/man/performance.metrics.Rd
OmicsMarkeR/man/performance.stats.Rd
OmicsMarkeR/man/perm.class.Rd
OmicsMarkeR/man/perm.features.Rd
OmicsMarkeR/man/pof.Rd
OmicsMarkeR/man/predictNewClasses.Rd
OmicsMarkeR/man/predicting.Rd
OmicsMarkeR/man/prediction.metrics.Rd
OmicsMarkeR/man/sequester.Rd
OmicsMarkeR/man/sorensen.Rd
OmicsMarkeR/man/spearman.Rd
OmicsMarkeR/man/svm.weights.Rd
OmicsMarkeR/man/svmrfeFeatureRanking.Rd
OmicsMarkeR/man/svmrfeFeatureRankingForMulticlass.Rd
OmicsMarkeR/man/training.Rd
OmicsMarkeR/man/tune.instructions.Rd
OmicsMarkeR/tests
OmicsMarkeR/tests/testthat
OmicsMarkeR/tests/testthat.R
OmicsMarkeR/tests/testthat/test_aggregation.R
OmicsMarkeR/tests/testthat/test_data_generation.R
OmicsMarkeR/tests/testthat/test_fs.ensembl.stability.R
OmicsMarkeR/tests/testthat/test_fs.stability.R
OmicsMarkeR/tests/testthat/test_stability_metrics.R
OmicsMarkeR/vignettes
OmicsMarkeR/vignettes/OmicsMarkeR-concordance.tex
OmicsMarkeR/vignettes/OmicsMarkeR.Rnw