ssizeRNA: Sample Size Calculation for RNA-Seq Experimental Design
Version 1.2.9

We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007) . We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use 'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.

Browse man pages Browse package API and functions Browse package files

AuthorRan Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Bioconductor views DNASeq DifferentialExpression ExperimentalDesign GeneExpression Microarray RNASeq Sequencing
Date of publication2017-01-09 10:00:34
MaintainerRan Bi <biran@iastate.edu>
LicenseGPL (>= 2)
Version1.2.9
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ssizeRNA")

Man pages

check.power: Average Power and True FDR Based on limma/voom RNAseq...
hammer.eset: RNA-seq data from Hammer, P. et al., 2010
sim.counts: RNA-seq Count Data Simulation from Negative-Binomial...
ssizeRNA_single: Sample Size Calculations for Two-Sample RNA-seq Experiments...
ssizeRNA_vary: Sample Size Calculations for Two-Sample RNA-seq Experiments...
ssize.twoSampVaryDelta: Sample Size Calculations for Two-Sample Microarray...

Functions

check.power Man page Source code
hammer.eset Man page
sim.counts Man page Source code
ssize.twoSampVaryDelta Man page Source code
ssizeRNA_single Man page Source code
ssizeRNA_vary Man page Source code

Files

inst
inst/NEWS.txt
inst/doc
inst/doc/ssizeRNA.R
inst/doc/ssizeRNA.Rnw
inst/doc/ssizeRNA.pdf
NAMESPACE
data
data/hammer.eset.RData
R
R/sim.counts.R
R/ssizeRNA_vary.R
R/ssize.twoSampVaryDelta.R
R/ssizeRNA_single.R
R/check.power.R
vignettes
vignettes/ssizeRNA_ref.bib
vignettes/ssizeRNA.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/check.power.Rd
man/ssizeRNA_vary.Rd
man/hammer.eset.Rd
man/ssizeRNA_single.Rd
man/ssize.twoSampVaryDelta.Rd
man/sim.counts.Rd
ssizeRNA documentation built on May 19, 2017, 3:32 p.m.