PROPER: PROspective Power Evaluation for RNAseq

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

Author
Hao Wu
Date of publication
None
Maintainer
Hao Wu <hao.wu@emory.edu>
License
GPL
Version
1.6.0

View on Bioconductor

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

Files in this package

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