iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

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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.

Author
Charlotte Soneson [aut, cre]
Date of publication
None
Maintainer
Charlotte Soneson <charlottesoneson@gmail.com>
License
GPL (>=2)
Version
1.2.0

View on Bioconductor

Man pages

basemethods
Accessor function for basemethods
calculate_adjp
Calculate adjusted p-values
calculate_performance
Calculate performance measures
COBRAapp
Interactive shiny app to visualize results
COBRAData
'COBRAData' object and constructor
cobradata_example
Example data set with three differential gene expression...
COBRAPerformance
'COBRAPerformance' object and constructor
COBRAPlot
'COBRAPlot' object and constructor
coerce
Convert an object to another class
corr
Accessor and replacement functions for 'corr' slot
deviation
Accessor and replacement functions for 'deviation' slot
Extract
Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot'...
facetted
Accessor and replacement functions for 'facetted' slot
fdrnbr
Accessor and replacement functions for 'fdrnbr' slot
fdrnbrcurve
Accessor and replacement functions for 'fdrnbrcurve' slot
fdrtpr
Accessor and replacement functions for 'fdrtpr' slot
fdrtprcurve
Accessor and replacement functions for 'fdrtprcurve' slot
fpc
Accessor and replacement functions for 'fpc' slot
fpr
Accessor and replacement functions for 'fpr' slot
maxsplit
Accessor and replacement functions for 'maxsplit' slot
onlyshared
Accessor and replacement functions for 'onlyshared' slot
overlap
Accessor and replacement functions for 'overlap' slot
padj
Accessor and replacement functions for 'padj' slot
plotcolors
Accessor and replacement functions for 'plotcolors' slot
plot_corr
Plot correlations
plot_deviation
Plot deviations
plot_fdrnbrcurve
Plot number of significant features vs FDR
plot_fdrtprcurve
Plot TPR vs FDR
plot_fpc
Plot FP curves
plot_fpr
Plot FPR
plot_overlap
Plot Venn diagram
plot_roc
Plot ROC curves
plot_scatter
Plot scatter plots
plot_tpr
Plot TPR
plot_upset
Create UpSet plots
prepare_data_for_plot
Prepare data for plotting
pval
Accessor and replacement functions for 'pval' slot
reorder_levels
Reorder levels in COBRAPlot object
roc
Accessor and replacement functions for 'roc' slot
scatter
Accessor and replacement functions for 'scatter' slot
score
Accessor and replacement functions for 'score' slot
splv
Accessor and replacement functions for 'splv' slot
stratiflevels
Accessor function for stratification levels
tpr
Accessor and replacement functions for 'tpr' slot
truth
Accessor and replacement functions for 'truth' slot

Files in this package

iCOBRA/DESCRIPTION
iCOBRA/NAMESPACE
iCOBRA/NEWS
iCOBRA/R
iCOBRA/R/AllGenerics.R
iCOBRA/R/COBRAData.R
iCOBRA/R/COBRAPerformance.R
iCOBRA/R/COBRAPlot.R
iCOBRA/R/calculate_performance.R
iCOBRA/R/cobradata_example.R
iCOBRA/R/helpers_general.R
iCOBRA/R/plot_methods.R
iCOBRA/R/printHead.R
iCOBRA/R/shiny.R
iCOBRA/README.md
iCOBRA/build
iCOBRA/build/vignette.rds
iCOBRA/data
iCOBRA/data/cobradata_example.rda
iCOBRA/inst
iCOBRA/inst/CITATION
iCOBRA/inst/doc
iCOBRA/inst/doc/iCOBRA.R
iCOBRA/inst/doc/iCOBRA.Rmd
iCOBRA/inst/doc/iCOBRA.html
iCOBRA/inst/extdata
iCOBRA/inst/extdata/about.md
iCOBRA/inst/extdata/cobradata_example_results.txt
iCOBRA/inst/extdata/cobradata_example_results_2.txt
iCOBRA/inst/extdata/cobradata_example_results_3.txt
iCOBRA/inst/extdata/cobradata_example_simres.Rdata
iCOBRA/inst/extdata/cobradata_example_truth.txt
iCOBRA/inst/extdata/instructions.md
iCOBRA/inst/extdata/screenshot_missing.png
iCOBRA/inst/extdata/screenshot_results.png
iCOBRA/inst/extdata/screenshot_truth.png
iCOBRA/man
iCOBRA/man/COBRAData.Rd
iCOBRA/man/COBRAPerformance.Rd
iCOBRA/man/COBRAPlot.Rd
iCOBRA/man/COBRAapp.Rd
iCOBRA/man/Extract.Rd
iCOBRA/man/basemethods.Rd
iCOBRA/man/calculate_adjp.Rd
iCOBRA/man/calculate_performance.Rd
iCOBRA/man/cobradata_example.Rd
iCOBRA/man/coerce.Rd
iCOBRA/man/corr.Rd
iCOBRA/man/deviation.Rd
iCOBRA/man/facetted.Rd
iCOBRA/man/fdrnbr.Rd
iCOBRA/man/fdrnbrcurve.Rd
iCOBRA/man/fdrtpr.Rd
iCOBRA/man/fdrtprcurve.Rd
iCOBRA/man/fpc.Rd
iCOBRA/man/fpr.Rd
iCOBRA/man/maxsplit.Rd
iCOBRA/man/onlyshared.Rd
iCOBRA/man/overlap.Rd
iCOBRA/man/padj.Rd
iCOBRA/man/plot_corr.Rd
iCOBRA/man/plot_deviation.Rd
iCOBRA/man/plot_fdrnbrcurve.Rd
iCOBRA/man/plot_fdrtprcurve.Rd
iCOBRA/man/plot_fpc.Rd
iCOBRA/man/plot_fpr.Rd
iCOBRA/man/plot_overlap.Rd
iCOBRA/man/plot_roc.Rd
iCOBRA/man/plot_scatter.Rd
iCOBRA/man/plot_tpr.Rd
iCOBRA/man/plot_upset.Rd
iCOBRA/man/plotcolors.Rd
iCOBRA/man/prepare_data_for_plot.Rd
iCOBRA/man/pval.Rd
iCOBRA/man/reorder_levels.Rd
iCOBRA/man/roc.Rd
iCOBRA/man/scatter.Rd
iCOBRA/man/score.Rd
iCOBRA/man/splv.Rd
iCOBRA/man/stratiflevels.Rd
iCOBRA/man/tpr.Rd
iCOBRA/man/truth.Rd
iCOBRA/tests
iCOBRA/tests/testthat
iCOBRA/tests/testthat.R
iCOBRA/tests/testthat/Rplots.pdf
iCOBRA/tests/testthat/test_app.R
iCOBRA/tests/testthat/test_calculate_adjp.R
iCOBRA/tests/testthat/test_calculate_performance.R
iCOBRA/tests/testthat/test_constructors.R
iCOBRA/tests/testthat/test_helpers.R
iCOBRA/tests/testthat/test_plots.R
iCOBRA/tests/testthat/test_results.txt
iCOBRA/tests/testthat/test_results_mod.txt
iCOBRA/tests/testthat/test_truth.txt
iCOBRA/vignettes
iCOBRA/vignettes/iCOBRA.Rmd
iCOBRA/vignettes/screenshot_COBRAapp.png