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Biocomb (version 0.4)

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

Description

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. 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. There exists the special function to deal with missing values, including different imputing schemes.

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Version

Install

install.packages('Biocomb')

Monthly Downloads

61

Version

0.4

License

GPL (>= 3)

Last Published

May 18th, 2018

Functions in Biocomb (0.4)

compute.aucs

Ranks the features
leukemia72_2

desease data
select.inf.symm

Ranks the features
leukemia_miss

desease data
pauclog

Calculates the p-values
plotRoc.curves

Plots the ROC curve for two-class problem
generate.data.miss

Generate the dataset with missing values
plotClass.result

Plots the results of classifier validation schemes
pauc

Calculates the p-values
select.forward.wrapper

Select the subset of features
select.forward.Corr

Select the subset of features
select.inf.gain

Ranks the features
select.relief

Ranks the features
select.inf.chi2

Ranks the features
select.fast.filter

Select the subset of features
select.cfs

Select the subset of features
select.process

Feature ranking and feature selection
CalculateHUM_Ex

Calculate HUM value
CalcROC

Calculate ROC points
CalculateHUM_Plot

Plot 2D-ROC curve
CalcGene

Calculate HUM value
CalculateHUM_seq

Calculate HUM value
ProcessData

Select the subset of features
CalculateHUM_ROC

Compute the points for ROC curve
chi2.algorithm

Select the subset of features
Calculate3D

Plot the 3D-ROC curve
cost.curve

Plots the RCC curve for two-class problem
Biocomb-package

Tools for Data Mining
compute.auc.random

Calculates the p-values
input_miss

Process the dataset with missing values
classifier.loop

Classification and classifier validation
data_test

simulated data
datasetF6

simulated data
leukemia72

desease data
compute.auc.permutation

Calculates the p-values