PROPER: PROspective Power Evaluation for RNAseq
Version 1.8.0

This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.

Browse man pages Browse package API and functions Browse package files

AuthorHao Wu
Bioconductor views DifferentialExpression RNASeq Sequencing
Date of publicationNone
MaintainerHao Wu <hao.wu@emory.edu>
LicenseGPL
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PROPER")

Man pages

comparePower: Compute the power-related quantities from simulation results
estParam: estimate simulation parameters from a count table
historicalData: Some existing RNA-seq and gene expression microarray data
plotPowerHist: Plot the histogram of power
plots: Plot the stratified curves for power-related quantities
power.seqDepth: Estimate the marginal power under different sequencing depth
RNAseq.SimOptions.2grp: Set up options for simulating RNA-seq data in two-group...
runSims: Run a number of RNA-seq simulations and DE detections
simRNAseq: Simulate RNA-seq count data
summaryPower: Generate a summary table for power analysis result

Functions

GE.human Man page
POWER1 Source code
RNAseq.SimOptions.2grp Man page Source code
add.axis1 Source code
bottomly Man page
cheung Man page
comparePower Man page Source code
estParam Man page Source code
getDisp1 Source code
getDisp2 Source code
gilad Man page
lfc.alt Source code
lfc.null Source code
makeMeanExpr.2grp Source code
maqc Man page
param Man page
pbmc Man page
plotAll Man page Source code
plotFDR Man page Source code
plotFDcost Man page Source code
plotPower Man page Source code
plotPowerAlpha Man page Source code
plotPowerFD Man page Source code
plotPowerHist Man page Source code
plotPowerTD Man page Source code
power.seqDepth Man page Source code
rnegbinom Source code
rowVars Source code
run.DESeq Source code
run.DSS Source code
run.edgeR Source code
runSims Man page Source code
setBaselineExpr Source code
setBaselineExpr.seqDepth Source code
setFC Source code
setOD Source code
simRNAseq Man page Source code
simRNAseq.2grp Source code
summaryPower Man page Source code
table2hist Source code
update.RNAseq.SimOptions.2grp Source code

Files

DESCRIPTION
NAMESPACE
R
R/DEdetection.R
R/estParam.R
R/plots.R
R/power.R
R/simOptions.2grp.R
R/simOptions.util.R
R/simfuns.R
build
build/vignette.rds
data
data/GE.human.RData
data/bottomly.RData
data/cheung.RData
data/datalist
data/gilad.RData
data/maqc.RData
data/pbmc.RData
doc
doc/NEWS
doc/PROPER.pdf
inst
inst/CITATION
inst/doc
inst/doc/PROPER.R
inst/doc/PROPER.Rnw
inst/doc/PROPER.pdf
man
man/RNAseq.SimOptions.2grp.Rd
man/comparePower.Rd
man/estParam.Rd
man/historicalData.Rd
man/plotPowerHist.Rd
man/plots.Rd
man/power.seqDepth.Rd
man/runSims.Rd
man/simRNAseq.Rd
man/summaryPower.Rd
vignettes
vignettes/FDC.pdf
vignettes/PROPER.Rnw
vignettes/TD.pdf
vignettes/all.pdf
vignettes/filter.pdf
vignettes/powers.pdf
PROPER documentation built on May 20, 2017, 10:06 p.m.