bootfs: Derive Robust Feature Sets for Two or Multiclass Classification Problems

In order to select a set of features used for successful classification of two or more groups of samples, multiple classification and feature selection algorithms are utilised. By combining the results of all methods and applying a bootstrapping approach a robust set of features with high power to distinguish the sample groups is selected.

AuthorChristian Bender
Date of publication2016-02-07 14:37:37
MaintainerChristian Bender <benderpkg@gmail.com>
LicenseGPL (>=2)
Version1.4.5

View on R-Forge

Man pages

align_feat_boruta: Create matrix with aligned feature sets from Boruta results.

align_features: Create matrix with aligned feature sets from SVM SCAD...

bootfs-package: Use multiple feature selection algorithms to derive robust...

bootstrap_roc: Create roc curves from bootstrapping classification results.

bsGBM: Wrapper for GBM bootstrapping

bsPAMR: Perform PAMR bootstrapping.

bsRFBORUTA: Perform RFBORUTA bootstrapping.

bsSCAD: Perform SCAD SVM bootstrapping.

bstr_multi: SVM SCAD bootstrapping classification and feature selection.

control_params: Create control parameter object for the classifiers

cvGBM: Make a crossvalidation using GBM.

cv_gbmclass: Internal crossvalidation method for GBM classification

cv_pamclass: Wrapper for PAMR classification call.

cvPAMR: Main wrapper to call PAMR crossvalidation.

cv_penalizedSVM: SVM SCAD crossvalidation.

cvRFBORUTA: Crossvalidation for Random Forests with Boruta feature...

cv_rfclass: Wrapper for RF Boruta classification crossvalidation.

cvSCAD: Crossvalidation for SCAD SVM classification and feature...

dist.eucsq: Squared euclidean distance metric. Used for ward clustering.

doBS: Perform bootstrapped feature selection with multiple...

doCV: Performance evaluation by crossvalidation for multiple...

drawheat: Wrapper for heatmap drawing.

extract_feat_boruta: Feature extraction for Boruta bootstrapping results.

extract_feat_pam: Feature extraction for PAMR bootstrapping results.

extract_feature_rankings: Feature ranking extraction for SVM SCAD bootstrapping...

extract_features: Helper for feature extraction.

extract_features_rf_boruta: Helper for feature extraction for RF Boruta.

extractsignatures: Helper for extracting all feature signatures from a...

fitGBM: Fit a Gradient Boosting Machine model.

gbm_multi: Calling function to GBM bootstrapping

get_ellipsis_a: Helper for importance graph drawing.

get_feature_ranking: Get a feature ranking. Helper for SVM SCAD feature...

get_pam_features: Helper for PAMR feature extraction.

importance_igraph: Graphically represent the (co-)occurrences of a set of...

layout.ellipsis: Layout function creating an ellipsis.

makeIG: Create an importance graph from a bootstrapping result of a...

resultBS: Summarise the results of a bootstrapping analysis.

resultCV: create a result plot for all performed crossvalidations

rf_multi: Wrapper for RF Boruta bootstrapping.

roc: Draw ROC curve.

run_pam: Wrapper for PAMR bootstrapping classification.

select_bootstrap_data: Select bootstrapping samples preserving group member...

select_cv_balanced: Balanced training/test set selection for crossvalidation.

select_threshold: Find optimal threshold for PAMR feature selection.

simDataSet: simDataSet - simulation of exemplary dataset

svmclass: Wrapper for SVM SCAD classification call.

ward: Clustering function using ward clustering.

Functions

align_feat_boruta Man page
align_features Man page
bootfs Man page
bootFS Man page
bootfs-package Man page
bootstrap_roc Man page
bsGBM Man page
bsPAMR Man page
bsRFBORUTA Man page
bsSCAD Man page
bstr_multi Man page
control_params Man page
cvGBM Man page
cv_gbmclass Man page
cv_pamclass Man page
cvPAMR Man page
cv_penalizedSVM Man page
cvRFBORUTA Man page
cv_rfclass Man page
cvSCAD Man page
dist.eucsq Man page
doBS Man page
doCV Man page
drawheat Man page
extract_feat_boruta Man page
extract_feat_pam Man page
extract_feature_rankings Man page
extract_features Man page
extract_features_rf_boruta Man page
extractsignatures Man page
fitGBM Man page
gbm_multi Man page
get_ellipsis_a Man page
get_feature_ranking Man page
get_pam_features Man page
importance_igraph Man page
layout.ellipsis Man page
makeIG Man page
resultBS Man page
resultCV Man page
rf_multi Man page
roc Man page
roc_binterval Man page
run_pam Man page
select_bootstrap_data Man page
select_cv_balanced Man page
select_threshold Man page
simDataSet Man page
svmclass Man page
ward Man page

Files

DESCRIPTION
NAMESPACE
R
R/align_feat_boruta.R R/align_features.R R/bootstrap_roc.R R/bsGBM.R R/bsPAMR.R R/bsRFBORUTA.R R/bsSCAD.R R/bs_methods.R R/control_params.R R/cvGBM.R R/cvPAMR.R R/cvRFBORUTA.R R/cvSCAD.R R/cv_gbmclass.R R/cv_pamclass.R R/cv_penalizedSVM.R R/cv_rfclass.R R/dist.eucsq.R R/doBS.R R/doCV.R R/drawheat.R R/extract_feat_boruta.R R/extract_feat_pam.R R/extract_feature_rankings.R R/extract_features.R R/extract_features_rf_boruta.R R/extractsignatures.R R/get_ellipsis_a.R R/get_feature_ranking.R R/get_pam_features.R R/importance_igraph.R R/layout.ellipsis.R R/makeIG.R R/resultBS.R R/resultCV.R R/roc.R R/select_bootstrap_data.R R/select_cv_balanced.R R/select_threshold.R R/simDataSet.R R/ward.R
build
build/vignette.rds
inst
inst/doc
inst/doc/bootfs.R
inst/doc/bootfs.Rnw
inst/doc/bootfs.pdf
man
man/align_feat_boruta.Rd man/align_features.Rd man/bootfs-package.Rd man/bootstrap_roc.Rd man/bsGBM.Rd man/bsPAMR.Rd man/bsRFBORUTA.Rd man/bsSCAD.Rd man/bstr_multi.Rd man/control_params.Rd man/cvGBM.Rd man/cvPAMR.Rd man/cvRFBORUTA.Rd man/cvSCAD.Rd man/cv_gbmclass.Rd man/cv_pamclass.Rd man/cv_penalizedSVM.Rd man/cv_rfclass.Rd man/dist.eucsq.Rd man/doBS.Rd man/doCV.Rd man/drawheat.Rd man/extract_feat_boruta.Rd man/extract_feat_pam.Rd man/extract_feature_rankings.Rd man/extract_features.Rd man/extract_features_rf_boruta.Rd man/extractsignatures.Rd man/fitGBM.Rd man/gbm_multi.Rd man/get_ellipsis_a.Rd man/get_feature_ranking.Rd man/get_pam_features.Rd man/importance_igraph.Rd man/layout.ellipsis.Rd man/makeIG.Rd man/resultBS.Rd man/resultCV.Rd man/rf_multi.Rd man/roc.Rd man/run_pam.Rd man/select_bootstrap_data.Rd man/select_cv_balanced.Rd man/select_threshold.Rd man/simDataSet.Rd man/svmclass.Rd man/ward.Rd
vignettes
vignettes/bootfs.Rnw
vignettes/impgraph1.pdf
vignettes/impgraph2.pdf
vignettes/references.bib
vignettes/resultbsmulti.pdf
vignettes/resultcvmulti.pdf
vignettes/rocpam.pdf
vignettes/rocrf.pdf
vignettes/rocscad.pdf

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

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