exprso: Rapid Implementation of Machine Learning Algorithms for Genomic Data

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.

AuthorThomas Quinn [aut, cre], Daniel Tylee [ctb]
Date of publication2016-12-23 17:35:21
MaintainerThomas Quinn <contacttomquinn@gmail.com>
LicenseGPL-2
Version0.1.8
http://github.com/tpq/exprso

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

Functions

array Man page
arrayExprs Man page
arrayMulti Man page
build Man page
build. Man page
buildANN Man page
buildANN,ExprsArray-method Man page
buildDNN Man page
buildDNN,ExprsArray-method Man page
buildEnsemble Man page
buildEnsemble,ExprsModel-method Man page
buildEnsemble,ExprsPipeline-method Man page
buildLDA Man page
buildLDA,ExprsArray-method Man page
buildNB Man page
buildNB,ExprsArray-method Man page
buildRF Man page
buildRF,ExprsArray-method Man page
buildSVM Man page
buildSVM,ExprsArray-method Man page
calcMonteCarlo Man page
calcNested Man page
calcStats Man page
calcStats,ExprsPredict-method Man page
check.ctrlGS Man page
compare Man page
compare,ExprsArray-method Man page
conjoin Man page
conjoin,ExprsArray-method Man page
conjoin,ExprsEnsemble-method Man page
conjoin,ExprsModel-method Man page
conjoin,ExprsPipeline-method Man page
ctrlFeatureSelect Man page
ctrlGridSearch Man page
ctrlSplitSet Man page
defaultArg Man page
doMulti Man page
doMulti,ExprsMulti-method Man page
[,ExprsArray,ANY,ANY,ANY-method Man page
ExprsArray-class Man page
[,ExprsArray-method Man page
$,ExprsArray-method Man page
ExprsBinary-class Man page
ExprsEnsemble-class Man page
ExprsMachine-class Man page
ExprsModel-class Man page
ExprsModule-class Man page
ExprsMulti-class Man page
exprso-predict Man page
[,ExprsPipeline,ANY,ANY,ANY-method Man page
ExprsPipeline-class Man page
[,ExprsPipeline-method Man page
$,ExprsPipeline-method Man page
ExprsPredict-class Man page
forceArg Man page
fs Man page
fs. Man page
fsANOVA Man page
fsANOVA,ExprsArray-method Man page
fsEbayes Man page
fsEbayes,ExprsBinary-method Man page
fsInclude Man page
fsInclude,ExprsBinary-method Man page
fsMrmre Man page
fsMrmre,ExprsBinary-method Man page
fsNULL Man page
fsNULL,ExprsArray-method Man page
fsPathClassRFE Man page
fsPathClassRFE,ExprsBinary-method Man page
fsPrcomp Man page
fsPrcomp,ExprsBinary-method Man page
fsSample Man page
fsSample,ExprsArray-method Man page
fsStats Man page
fsStats,ExprsBinary-method Man page
getArgs Man page
getFeatures Man page
getFeatures,ExprsArray-method Man page
getFeatures,ExprsEnsemble-method Man page
getFeatures,ExprsModel-method Man page
getFeatures,ExprsPipeline-method Man page
GSE2eSet Man page
makeGridFromArgs Man page
modCluster Man page
modCluster,ExprsArray-method Man page
modFilter Man page
modFilter,ExprsArray-method Man page
modHistory Man page
modHistory,ExprsArray-method Man page
modNormalize Man page
modNormalize,ExprsArray-method Man page
modSubset Man page
modSwap Man page
modSwap,ExprsBinary-method Man page
modTransform Man page
modTransform,ExprsArray-method Man page
pipeFilter Man page
pipeFilter,ExprsPipeline-method Man page
pipeSubset Man page
pipeUnboot Man page
pipeUnboot,ExprsPipeline-method Man page
plCV Man page
plGrid Man page
plGridMulti Man page
plMonteCarlo Man page
plNested Man page
plot,ExprsArray,missing-method Man page
predict,ExprsEnsemble-method Man page
predict,ExprsMachine-method Man page
predict,ExprsModule-method Man page
reRank Man page
show,ExprsArray-method Man page
show,ExprsEnsemble-method Man page
show,ExprsModel-method Man page
show,ExprsPipeline-method Man page
show,ExprsPredict-method Man page
split Man page
splitSample Man page
splitSample,ExprsArray-method Man page
splitStratify Man page
splitStratify,ExprsArray-method Man page
subset,ExprsArray-method Man page
subset,ExprsPipeline-method Man page
summary,ExprsArray-method Man page
summary,ExprsPipeline-method Man page
testSet Man page
trainingSet Man page
validationSet Man page

Files

exprso
exprso/inst
exprso/inst/CITATION
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

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