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

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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).

Author
Yudi Pawitan <Yudi.Pawitan@ki.se> and Alexander Ploner <Alexander.Ploner@ki.se>
Date of publication
None
Maintainer
Alexander Ploner <Alexander.Ploner@ki.se>
License
LGPL
Version
1.48.0

View on Bioconductor

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

Files in this package

OCplus/DESCRIPTION
OCplus/NAMESPACE
OCplus/R
OCplus/R/CDF.R
OCplus/R/EOC.R
OCplus/R/FDR.R
OCplus/R/OCshow.R
OCplus/R/Simulations.R
OCplus/R/TOC.R
OCplus/R/localfdr.R
OCplus/R/localfdr1d.R
OCplus/R/localfdr2d.R
OCplus/R/pdf.R
OCplus/R/samplesize.R
OCplus/R/tMixture.R
OCplus/build
OCplus/build/vignette.rds
OCplus/inst
OCplus/inst/doc
OCplus/inst/doc/OCplus.R
OCplus/inst/doc/OCplus.Rnw
OCplus/inst/doc/OCplus.pdf
OCplus/man
OCplus/man/DrawContourlines.Rd
OCplus/man/EOC.Rd
OCplus/man/FDR.Rd
OCplus/man/MAsim.smyth.Rd
OCplus/man/OCshow.Rd
OCplus/man/TOC.Rd
OCplus/man/Undocumented.Rd
OCplus/man/average.fdr.Rd
OCplus/man/fdr1d.Rd
OCplus/man/fdr2d.Rd
OCplus/man/plot.FDR.result.Rd
OCplus/man/plot.fdr1d.result.Rd
OCplus/man/plot.fdr2d.result.Rd
OCplus/man/samplesize.Rd
OCplus/man/smooth1d.Rd
OCplus/man/summary.fdr.result.Rd
OCplus/man/tMixture.Rd
OCplus/man/tstatistics.Rd
OCplus/vignettes
OCplus/vignettes/OCplus.Rnw
OCplus/vignettes/OCplus.bib