OCplus: Operating characteristics plus sample size and local fdr for microarray experiments
Version 1.50.0

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).

Browse man pages Browse package API and functions Browse package files

AuthorYudi Pawitan <Yudi.Pawitan@ki.se> and Alexander Ploner <Alexander.Ploner@ki.se>
Bioconductor views DifferentialExpression Microarray MultipleComparison
Date of publicationNone
MaintainerAlexander Ploner <Alexander.Ploner@ki.se>
LicenseLGPL
Version1.50.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("OCplus")

Man pages

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

Functions

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

Files

DESCRIPTION
NAMESPACE
R
R/CDF.R
R/EOC.R
R/FDR.R
R/OCshow.R
R/Simulations.R
R/TOC.R
R/localfdr.R
R/localfdr1d.R
R/localfdr2d.R
R/pdf.R
R/samplesize.R
R/tMixture.R
build
build/vignette.rds
inst
inst/doc
inst/doc/OCplus.R
inst/doc/OCplus.Rnw
inst/doc/OCplus.pdf
man
man/DrawContourlines.Rd
man/EOC.Rd
man/FDR.Rd
man/MAsim.smyth.Rd
man/OCshow.Rd
man/TOC.Rd
man/Undocumented.Rd
man/average.fdr.Rd
man/fdr1d.Rd
man/fdr2d.Rd
man/plot.FDR.result.Rd
man/plot.fdr1d.result.Rd
man/plot.fdr2d.result.Rd
man/samplesize.Rd
man/smooth1d.Rd
man/summary.fdr.result.Rd
man/tMixture.Rd
man/tstatistics.Rd
vignettes
vignettes/OCplus.Rnw
vignettes/OCplus.bib
vignettes/pix
OCplus documentation built on May 20, 2017, 9:22 p.m.