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iCOBRA (version 1.0.2)

Comparison and Visualization of Ranking and Assignment Methods

Description

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results.

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Version

Version

1.0.2

License

GPL (>=2)

Maintainer

Charlotte Soneson

Last Published

February 15th, 2017

Functions in iCOBRA (1.0.2)

Subsetting COBRAData, COBRAPerformance or COBRAPlot objects

Create UpSet plots

Interactive shiny app to visualize results

Plot correlations

COBRAPlot-class

COBRAPlot object and constructor

Accessor and replacement functions for facetted slot

Accessor and replacement functions for onlyshared slot

Accessor and replacement functions for fpr slot

Accessor and replacement functions for pval slot

Accessor and replacement functions for maxsplit slot

calculate_performance

Calculate performance measures

Accessor and replacement functions for scatter slot

Accessor and replacement functions for padj slot

Calculate adjusted p-values

COBRAPerformance-class

COBRAPerformance object and constructor

Accessor and replacement functions for fdrtprcurve slot

Accessor and replacement functions for deviation slot

Accessor and replacement functions for tpr slot

Accessor and replacement functions for fpc slot

Accessor and replacement functions for fdrnbr slot

Plot Venn diagram

Accessor and replacement functions for corr slot

plot_fdrtprcurve

Plot TPR vs FDR

Accessor and replacement functions for fdrtpr slot

Accessor and replacement functions for roc slot

Plot ROC curves

Accessor function for basemethods

Accessor and replacement functions for overlap slot

Plot scatter plots

Accessor and replacement functions for plotcolors slot

Convert an object to another class

Accessor and replacement functions for fdrnbrcurve slot

Reorder levels in COBRAPlot object

cobradata_example

Example data set with three differential gene expression methods

COBRAData-class

COBRAData object and constructor

prepare_data_for_plot

Prepare data for plotting

plot_fdrnbrcurve

Plot number of significant features vs FDR

Accessor and replacement functions for score slot

Plot deviations

Accessor and replacement functions for truth slot

Accessor function for stratification levels

Accessor and replacement functions for splv slot