Package: OCplus 1.87.0

Alexander Ploner

OCplus: Operating characteristics plus sample size and local fdr for microarray experiments

This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).

Authors:Yudi Pawitan <[email protected]> and Alexander Ploner <[email protected]>

OCplus_1.87.0.tar.gz
OCplus_1.87.0.zip(r-4.7)OCplus_1.87.0.zip(r-4.6)OCplus_1.87.0.zip(r-4.5)
OCplus_1.87.0.tgz(r-4.6-any)OCplus_1.87.0.tgz(r-4.5-any)
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OCplus_1.87.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OCplus/json (API)

# Install 'OCplus' in R:

install.packages('OCplus', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:OCplus-1.87.0(bioc 3.24)OCplus-1.86.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray differentialexpression multiplecomparison

4.08 score 2 scripts 6 mentions 49 exports 12 dependencies

Last updated from:2b53caf23d. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	144
linux-devel-x86_64	NOTE	208
source / vignettes	OK	195
linux-release-x86_64	NOTE	221
macos-release-arm64	NOTE	99
macos-oldrel-arm64	NOTE	87
windows-devel	NOTE	99
windows-release	NOTE	111
windows-oldrel	NOTE	104
wasm-release	OK	125

Exports:approx2d average.fdr brk2mid CDF CDF.paired CDFmix CDFmix.paired df2var dgfree dmt dmt.paired dmtmix dmtmix.paired DoConstrain DrawContourlines EOC FDR FDR.paired fdr1d fdr2d FDRp gausei lfdr lfdr.paired MAsim MAsim.real MAsim.smyth MAsim.var MidBreaks MidBreaks.t OCshow p0 PermNull plot.FDR.result plot.fdr1d.result plot.fdr2d.result Rinv rmatrix samplesize smooth1d smooth2d.basic smooth2d.direct summary.fdr.result tMixture TOC topDE Tornadoplot tstatistics Volcanoplot

Dependencies:Biobase BiocGenerics deldir generics interp lattice MASS Matrix multtest Rcpp RcppEigen survival

OCplus Introduction

Rendered fromOCplus.Rnwusingutils::Sweave

Last update: 2022-10-14
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Average a two-dimensional local false discovery rate	average.fdr
Draw and label a set of pre-calculated isolines	DrawContourlines
Estimated or empirical FDR, sensitivity, etc as a function of cutoff level	EOC FDRp
Compute FDR for general scenarios	CDF CDF.paired CDFmix CDFmix.paired FDR FDR.paired
Compute classical local false discovery rate	fdr1d
Compute two-dimensional local false discovery rate	fdr2d
Simulate two-sample microarray data	MAsim MAsim.real MAsim.smyth MAsim.var
Show one ore several OC curves graphically	OCshow
Plot the empirical FDR as a function of the cutoff level	plot.FDR.result
Plot univariate local false discovery output	plot.fdr1d.result
Plotting the bivariate local false discovery results	plot.fdr2d.result Tornadoplot Volcanoplot
FDR as a function of sample size	samplesize
Smoothing a vector of counts	smooth1d
Display functions for local fdr output	p0 summary.fdr.result topDE
Fit a mixture of t-distributions	tMixture
Theoretical FDR and sensitivity as a function of cutoff level	TOC
Compute multiple parallel t-statistics	PermNull tstatistics