exprso: Rapid Implementation of Machine Learning Algorithms for Genomic Data

Share:

Supervised machine learning has an increasingly important role in biological studies. However, the sheer complexity of classification pipelines poses a significant barrier to the expert biologist unfamiliar with machine learning. Moreover, many biologists lack the time or technical skills necessary to establish their own pipelines. This package introduces a framework for the rapid implementation of high-throughput supervised machine learning built with the biologist user in mind. Written by biologists, for biologists, this package provides a user-friendly interface that empowers investigators to execute state-of-the-art binary and multi-class classification, including deep learning, with minimal programming experience necessary.

Author
Thomas Quinn [aut, cre], Daniel Tylee [ctb]
Date of publication
2016-09-27 16:39:46
Maintainer
Thomas Quinn <contacttomquinn@gmail.com>
License
GPL-2
Version
0.1.7
URLs

View on CRAN

Man pages

array
Sample ExprsBinary Data
arrayExprs
Import Data as ExprsArray
arrayMulti
Sample ExprsMulti Data
build
Build Classifiers
build.
Workhorse for build Methods
buildEnsemble
Build Ensemble
calcMonteCarlo
Calculate 'plMonteCarlo' Performance
calcNested
Calculate 'plNested' Performance
calcStats
Calculate Classifier Performance
check.ctrlGS
Check 'ctrlGS' Arguments
compare
Compare 'ExprsArray' Objects
conjoin
Combine 'exprso' Objects
ctrlFeatureSelect
Manage 'fs' Arguments
ctrlGridSearch
Manage 'plGrid' Arguments
ctrlSplitSet
Manage 'split' Arguments
defaultArg
Set an args List Element to Default Value
doMulti
Perform "1 vs. all" Task
ExprsArray-class
An S4 class to store feature and annotation data
ExprsBinary-class
An S4 class to store feature and annotation data
ExprsEnsemble-class
An S4 class to store multiple classification models
ExprsMachine-class
An S4 class to store the classification model
ExprsModel-class
An S4 class to store the classification model
ExprsModule-class
An S4 class to store the classification model
ExprsMulti-class
An S4 class to store feature and annotation data
exprso-predict
Predict Class Labels
ExprsPipeline-class
An S4 class to store models built during high-throughput...
ExprsPredict-class
An S4 class to store class predictions
forceArg
Force an args List Element to Value
fs
Perform Feature Selection
fs.
Workhorse for fs Methods
getArgs
Build an args List
getFeatures
Retrieve Feature Set
GSE2eSet
Convert GSE to eSet
makeGridFromArgs
Build Argument Grid
modCluster
Cluster Subjects
modFilter
Hard Filter Data
modHistory
Duplicate Feature Selection History
modNormalize
Normalize Data
modSubset
Tidy Subset Wrapper
modSwap
Swap Case Subjects
modTransform
Log Transform Data
pipeFilter
Filter 'ExprsPipeline' Object
pipeUnboot
Rename "boot" Column
plCV
Perform Simple Cross-Validation
plGrid
Perform High-Throughput Classification
plGridMulti
Perform High-Throughput Classification
plMonteCarlo
Monte Carlo Cross-Validation
plNested
Nested Cross-Validation
reRank
Serialize "1 vs. all" Feature Selection
split
split 'ExprsArray' objects
trainingSet
Extract Training Set
validationSet
Extract Validation Set

Files in this package

exprso
exprso/inst
exprso/inst/doc
exprso/inst/doc/cheatsheet.Rmd
exprso/inst/doc/readme.Rmd
exprso/inst/doc/readme.html
exprso/inst/doc/advanced-vignette.Rmd
exprso/inst/doc/introduction-vignette.Rmd
exprso/inst/doc/advanced-vignette.R
exprso/inst/doc/introduction-vignette.html
exprso/inst/doc/introduction-vignette.R
exprso/inst/doc/advanced-vignette.html
exprso/inst/doc/cheatsheet.R
exprso/inst/doc/cheatsheet.html
exprso/tests
exprso/tests/testthat.R
exprso/tests/testthat
exprso/tests/testthat/test-mod.R
exprso/tests/testthat/test-pl-cv.R
exprso/tests/testthat/test-fs.R
exprso/tests/testthat/test-pl-multi.R
exprso/tests/testthat/test-ens.R
exprso/tests/testthat/test-build.R
exprso/tests/testthat/test-pl-gs.R
exprso/tests/testthat/test-split.R
exprso/tests/testthat/data.RData
exprso/tests/testthat/test-compare.R
exprso/NAMESPACE
exprso/NEWS.md
exprso/data
exprso/data/arrayMulti.rda
exprso/data/array.rda
exprso/R
exprso/R/5.3-doMulti.R
exprso/R/1.1-classes.R
exprso/R/2.2-process.R
exprso/R/8.2-ens.R
exprso/R/6-predict.R
exprso/R/5.1-fs.R
exprso/R/4.3-compare.R
exprso/R/8.1-pipe.R
exprso/R/5.2-build.R
exprso/R/7.3-plGridMulti.R
exprso/R/9-tidy.R
exprso/R/4.2-modCluster.R
exprso/R/7.1-plCV.R
exprso/R/3.2-conjoin.R
exprso/R/7.5-plNested.R
exprso/R/2.1-import.R
exprso/R/3.1-split.R
exprso/R/4.1-modSwap.R
exprso/R/7.4-plMonteCarlo.R
exprso/R/9-global.R
exprso/R/1.2-methods.R
exprso/R/7.2-plGrid.R
exprso/vignettes
exprso/vignettes/cheatsheet.Rmd
exprso/vignettes/readme.Rmd
exprso/vignettes/advanced-vignette.Rmd
exprso/vignettes/exprso-diagram.jpg
exprso/vignettes/introduction-vignette.Rmd
exprso/vignettes/exprso-diagram.cmap
exprso/README.md
exprso/MD5
exprso/build
exprso/build/vignette.rds
exprso/DESCRIPTION
exprso/man
exprso/man/getFeatures.Rd
exprso/man/ExprsPredict-class.Rd
exprso/man/validationSet.Rd
exprso/man/pipeUnboot.Rd
exprso/man/build..Rd
exprso/man/modFilter.Rd
exprso/man/arrayMulti.Rd
exprso/man/ExprsMulti-class.Rd
exprso/man/modSwap.Rd
exprso/man/modCluster.Rd
exprso/man/modHistory.Rd
exprso/man/modSubset.Rd
exprso/man/calcNested.Rd
exprso/man/exprso-predict.Rd
exprso/man/makeGridFromArgs.Rd
exprso/man/ExprsModule-class.Rd
exprso/man/plGrid.Rd
exprso/man/ExprsModel-class.Rd
exprso/man/forceArg.Rd
exprso/man/ctrlGridSearch.Rd
exprso/man/reRank.Rd
exprso/man/modTransform.Rd
exprso/man/plMonteCarlo.Rd
exprso/man/split.Rd
exprso/man/ExprsEnsemble-class.Rd
exprso/man/GSE2eSet.Rd
exprso/man/pipeFilter.Rd
exprso/man/fs.Rd
exprso/man/ExprsMachine-class.Rd
exprso/man/arrayExprs.Rd
exprso/man/buildEnsemble.Rd
exprso/man/ExprsPipeline-class.Rd
exprso/man/ctrlFeatureSelect.Rd
exprso/man/array.Rd
exprso/man/modNormalize.Rd
exprso/man/compare.Rd
exprso/man/check.ctrlGS.Rd
exprso/man/ExprsArray-class.Rd
exprso/man/calcMonteCarlo.Rd
exprso/man/build.Rd
exprso/man/plGridMulti.Rd
exprso/man/doMulti.Rd
exprso/man/fs..Rd
exprso/man/conjoin.Rd
exprso/man/plCV.Rd
exprso/man/ExprsBinary-class.Rd
exprso/man/plNested.Rd
exprso/man/ctrlSplitSet.Rd
exprso/man/calcStats.Rd
exprso/man/trainingSet.Rd
exprso/man/defaultArg.Rd
exprso/man/getArgs.Rd