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
Version1.8.1
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

Functions

aggregation Man page
bagging.wrapper Man page
canberra Man page
canberra_stability Man page
CLA Man page
create.corr.matrix Man page
create.discr.matrix Man page
create.random.matrix Man page
denovo.grid Man page
EE Man page
EM Man page
ES Man page
extract.args Man page
extract.features Man page
feature.table Man page
fit.only.model Man page
fs.ensembl.stability Man page
fs.stability Man page
jaccard Man page
kuncheva Man page
modelList Man page
modelTuner Man page
modelTuner_loo Man page
noise.matrix Man page
ochiai Man page
optimize.model Man page
pairwise.model.stability Man page
pairwise.stability Man page
params Man page
perf.calc Man page
performance.metrics Man page
performance.stats Man page
perm.class Man page
perm.features Man page
pof Man page
predicting Man page
prediction.metrics Man page
predictNewClasses Man page
RPT Man page
sequester Man page
sorensen Man page
spearman Man page
svmrfeFeatureRanking Man page
svmrfeFeatureRankingForMulticlass Man page
svm.weights Man page
training Man page
tune.instructions Man page

Files

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/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.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.