OmicsMarkeR: Classification and Feature Selection for 'Omics' Datasets

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.

AuthorCharles E. Determan Jr. <cdetermanjr@gmail.com>
Date of publicationNone
MaintainerCharles E. Determan Jr. <cdetermanjr@gmail.com>
LicenseGPL-3
Version1.6.0
http://github.com/cdeterman/OmicsMarkeR

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

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