iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("iCOBRA")
AuthorCharlotte Soneson [aut, cre]
Bioconductor views Classification
Date of publicationNone
MaintainerCharlotte Soneson <charlottesoneson@gmail.com>
LicenseGPL (>=2)
Version1.2.0

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

Functions

[ Man page
basemethods Man page
basemethods,COBRAPerformance-method Man page
basemethods,COBRAPlot-method Man page
calculate_adjp Man page
calculate_performance Man page
COBRAapp Man page
COBRAData Man page
.COBRAData Man page
COBRAData-class Man page
cobradata_example Man page
COBRAData_from_text Man page
[,COBRAData-method Man page
COBRAData_to_text Man page
COBRAPerformance Man page
.COBRAPerformance Man page
COBRAPerformance-class Man page
[,COBRAPerformance-method Man page
COBRAPlot Man page
.COBRAPlot Man page
COBRAPlot-class Man page
COBRAPlot,COBRAPerformance-method Man page
[,COBRAPlot-method Man page
coerce Man page
coerce, Man page
coerce,COBRAPerformance,COBRAPlot-method Man page
coerce,COBRAPlot,COBRAPerformance-method Man page
corr Man page
corr<- Man page
corr<-,COBRAPerformance,data.frame-method Man page
corr,COBRAPerformance-method Man page
corr<-,COBRAPlot,data.frame-method Man page
corr,COBRAPlot-method Man page
deviation Man page
deviation<- Man page
deviation<-,COBRAPerformance,data.frame-method Man page
deviation,COBRAPerformance-method Man page
deviation<-,COBRAPlot,data.frame-method Man page
deviation,COBRAPlot-method Man page
Extract Man page
facetted Man page
facetted<- Man page
facetted<-,COBRAPlot,logical-method Man page
facetted,COBRAPlot-method Man page
fdrnbr Man page
fdrnbr<- Man page
fdrnbr<-,COBRAPerformance,data.frame-method Man page
fdrnbr,COBRAPerformance-method Man page
fdrnbr<-,COBRAPlot,data.frame-method Man page
fdrnbr,COBRAPlot-method Man page
fdrnbrcurve Man page
fdrnbrcurve<- Man page
fdrnbrcurve<-,COBRAPerformance,data.frame-method Man page
fdrnbrcurve,COBRAPerformance-method Man page
fdrnbrcurve<-,COBRAPlot,data.frame-method Man page
fdrnbrcurve,COBRAPlot-method Man page
fdrtpr Man page
fdrtpr<- Man page
fdrtpr<-,COBRAPerformance,data.frame-method Man page
fdrtpr,COBRAPerformance-method Man page
fdrtpr<-,COBRAPlot,data.frame-method Man page
fdrtpr,COBRAPlot-method Man page
fdrtprcurve Man page
fdrtprcurve<- Man page
fdrtprcurve<-,COBRAPerformance,data.frame-method Man page
fdrtprcurve,COBRAPerformance-method Man page
fdrtprcurve<-,COBRAPlot,data.frame-method Man page
fdrtprcurve,COBRAPlot-method Man page
fpc Man page
fpc<- Man page
fpc<-,COBRAPerformance,data.frame-method Man page
fpc,COBRAPerformance-method Man page
fpc<-,COBRAPlot,data.frame-method Man page
fpc,COBRAPlot-method Man page
fpr Man page
fpr<- Man page
fpr<-,COBRAPerformance,data.frame-method Man page
fpr,COBRAPerformance-method Man page
fpr<-,COBRAPlot,data.frame-method Man page
fpr,COBRAPlot-method Man page
maxsplit Man page
maxsplit<- Man page
maxsplit,COBRAPerformance-method Man page
maxsplit<-,COBRAPerformance,numeric-method Man page
maxsplit,COBRAPlot-method Man page
maxsplit<-,COBRAPlot,numeric-method Man page
onlyshared Man page
onlyshared<- Man page
onlyshared<-,COBRAPerformance,logical-method Man page
onlyshared,COBRAPerformance-method Man page
onlyshared<-,COBRAPlot,logical-method Man page
onlyshared,COBRAPlot-method Man page
overlap Man page
overlap<- Man page
overlap<-,COBRAPerformance,list_df-method Man page
overlap,COBRAPerformance-method Man page
overlap<-,COBRAPlot,list_df-method Man page
overlap,COBRAPlot-method Man page
padj Man page
padj<- Man page
padj<-,COBRAData,data.frame-method Man page
padj,COBRAData-method Man page
plotcolors Man page
plotcolors<- Man page
plotcolors<-,COBRAPlot,character-method Man page
plotcolors,COBRAPlot-method Man page
plot_corr Man page
plot_deviation Man page
plot_fdrnbrcurve Man page
plot_fdrtprcurve Man page
plot_fpc Man page
plot_fpr Man page
plot_overlap Man page
plot_roc Man page
plot_scatter Man page
plot_tpr Man page
plot_upset Man page
prepare_data_for_plot Man page
pval Man page
pval<- Man page
pval<-,COBRAData,data.frame-method Man page
pval,COBRAData-method Man page
reorder_levels Man page
roc Man page
roc<- Man page
roc<-,COBRAPerformance,data.frame-method Man page
roc,COBRAPerformance-method Man page
roc<-,COBRAPlot,data.frame-method Man page
roc,COBRAPlot-method Man page
\S4method{[}{COBRAData,ANY,ANY} Man page
\S4method{[}{COBRAData,ANY,ANY,ANY} Man page
\S4method{[}{COBRAPerformance,ANY,ANY} Man page
\S4method{[}{COBRAPerformance,ANY,ANY,ANY} Man page
\S4method{[}{COBRAPlot,ANY,ANY} Man page
\S4method{[}{COBRAPlot,ANY,ANY,ANY} Man page
scatter Man page
scatter<- Man page
scatter<-,COBRAPerformance,data.frame-method Man page
scatter,COBRAPerformance-method Man page
scatter<-,COBRAPlot,data.frame-method Man page
scatter,COBRAPlot-method Man page
score Man page
score<- Man page
score<-,COBRAData,data.frame-method Man page
score,COBRAData-method Man page
splv Man page
splv<- Man page
splv<-,COBRAPerformance,character-method Man page
splv,COBRAPerformance-method Man page
splv<-,COBRAPlot,character-method Man page
splv,COBRAPlot-method Man page
stratiflevels Man page
stratiflevels,COBRAPerformance-method Man page
stratiflevels,COBRAPlot-method Man page
tpr Man page
tpr<- Man page
tpr<-,COBRAPerformance,data.frame-method Man page
tpr,COBRAPerformance-method Man page
tpr<-,COBRAPlot,data.frame-method Man page
tpr,COBRAPlot-method Man page
truth Man page
truth<- Man page
truth<-,COBRAData,data.frame-method Man page
truth,COBRAData-method Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.