Biocomb: Feature Selection and Classification with the Embedded Validation Procedures for Biomedical Data Analysis

Contains functions for the data analysis with the emphasis on biological data, including several algorithms for feature ranking, feature selection, classification algorithms with the embedded validation procedures. The functions can deal with numerical as well as with nominal features. Includes also the functions for calculation of feature AUC (Area Under the ROC Curve) and HUM (hypervolume under manifold) values and construction 2D- and 3D- ROC curves. Biocomb provides the calculation of Area Above the RCC (AAC) values and construction of Relative Cost Curves (RCC) to estimate the classifier performance under unequal misclassification costs problem. Biocomb has the special function to deal with missing values, including different imputing schemes.

Author
Natalia Novoselova,Junxi Wang,Frank Pessler,Frank Klawonn
Date of publication
2015-11-27 08:53:04
Maintainer
Natalia Novoselova <novos65@mail.ru>
License
GPL (>= 3)
Version
0.2

View on CRAN

Man pages

Biocomb-package
Tools for Data Mining
CalcGene
Calculate HUM value
CalcROC
Calculate ROC points
Calculate3D
Plot the 3D-ROC curve
CalculateHUM_Ex
Calculate HUM value
CalculateHUM_Plot
Plot 2D-ROC curve
CalculateHUM_ROC
Compute the points for ROC curve
CalculateHUM_seq
Calculate HUM value
chi2.algorithm
Select the subset of features
classifier.loop
Classification and classifier validation
compute.auc.permutation
Calculates the p-values
compute.auc.random
Calculates the p-values
compute.aucs
Ranks the features
cost.curve
Plots the RCC curve for two-class problem
datasetF6
simulated data
data_test
simulated data
generate.data.miss
Generate the dataset with missing values
input_miss
Process the dataset with missing values
leukemia72
desease data
leukemia72_2
desease data
leukemia_miss
desease data
pauc
Calculates the p-values
pauclog
Calculates the p-values
plotClass.result
Plots the results of classifier validation schemes
plotRoc.curves
Plots the ROC curve for two-class problem
ProcessData
Select the subset of features
select.cfs
Select the subset of features
select.fast.filter
Select the subset of features
select.forward.Corr
Select the subset of features
select.forward.wrapper
Select the subset of features
select.inf.chi2
Ranks the features
select.inf.gain
Ranks the features
select.inf.symm
Ranks the features
select.process
Feature ranking and feature selection
select.relief
Ranks the features

Files in this package

Biocomb
Biocomb/src
Biocomb/src/CorrF.cpp
Biocomb/src/CHI2.cpp
Biocomb/src/HUMseq.cpp
Biocomb/src/RcppExports.cpp
Biocomb/NAMESPACE
Biocomb/data
Biocomb/data/datasetF6.txt.gz
Biocomb/data/leukemia72.txt.gz
Biocomb/data/leukemia_miss.txt.gz
Biocomb/data/data_test.txt.gz
Biocomb/data/leukemia72_2.txt.gz
Biocomb/R
Biocomb/R/select.feature.info.R
Biocomb/R/plotClass.result.R
Biocomb/R/class_cross.R
Biocomb/R/ROC_Plot.R
Biocomb/R/Sub.filename.R
Biocomb/R/CalculateHUM_Ex.R
Biocomb/R/input_miss.R
Biocomb/R/RcppExports.R
Biocomb/R/CalculateHUM_ROC.R
Biocomb/R/CalculateHUM_seq.R
Biocomb/R/plotRoc.curves.R
Biocomb/R/compute.auc.pvalues.R
Biocomb/R/pauc.R
Biocomb/R/char.to.numeric.R
Biocomb/R/rcc.aac.R
Biocomb/MD5
Biocomb/DESCRIPTION
Biocomb/man
Biocomb/man/datasetF6.Rd
Biocomb/man/compute.auc.permutation.Rd
Biocomb/man/select.forward.Corr.Rd
Biocomb/man/select.inf.symm.Rd
Biocomb/man/select.inf.gain.Rd
Biocomb/man/CalcROC.Rd
Biocomb/man/pauclog.Rd
Biocomb/man/Calculate3D.Rd
Biocomb/man/select.cfs.Rd
Biocomb/man/generate.data.miss.Rd
Biocomb/man/input_miss.Rd
Biocomb/man/ProcessData.Rd
Biocomb/man/leukemia72_2.Rd
Biocomb/man/leukemia72.Rd
Biocomb/man/select.inf.chi2.Rd
Biocomb/man/chi2.algorithm.Rd
Biocomb/man/data_test.Rd
Biocomb/man/CalculateHUM_Ex.Rd
Biocomb/man/select.forward.wrapper.Rd
Biocomb/man/plotRoc.curves.Rd
Biocomb/man/select.fast.filter.Rd
Biocomb/man/CalculateHUM_seq.Rd
Biocomb/man/leukemia_miss.Rd
Biocomb/man/CalculateHUM_ROC.Rd
Biocomb/man/select.process.Rd
Biocomb/man/compute.auc.random.Rd
Biocomb/man/plotClass.result.Rd
Biocomb/man/pauc.Rd
Biocomb/man/select.relief.Rd
Biocomb/man/classifier.loop.Rd
Biocomb/man/cost.curve.Rd
Biocomb/man/CalculateHUM_Plot.Rd
Biocomb/man/Biocomb-package.Rd
Biocomb/man/CalcGene.Rd
Biocomb/man/compute.aucs.Rd