PoissonSeq: Significance analysis of sequencing data based on a Poisson log linear model
Version 1.1.2

This package implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data. The description of the method is in Li J, Witten DM, Johnstone I, Tibshirani R (2012). Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 13(3): 523-38. We estimate the sequencing depths of experiments using a new method based on Poisson goodness-of-fit statistic, calculate a score statistic on the basis of a Poisson log-linear model, and then estimate the false discovery rate using a modified version of permutation plug-in method. A more detailed instruction as well as sample data is available at http://www.stanford.edu/~junli07/research.html. In this version, we changed the way of calculating log foldchange for two-class data. The FDR estimation part remains unchanged.

AuthorJun Li
Date of publication2012-10-10 15:36:34
MaintainerJun Li <jun.li@nd.edu>
LicenseGPL (>= 2)
Version1.1.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PoissonSeq")

Popular man pages

dat: A toy RNA-Seq data.
PS.Est.Depth: estimate the sequencing depths
PS.Main: detecting differentially expressed genes from RNA-Seq data.
See all...

All man pages Function index File listing

Man pages

dat: A toy RNA-Seq data.
PS.Est.Depth: estimate the sequencing depths
PS.Main: detecting differentially expressed genes from RNA-Seq data.

Functions

Check.Argu.Dat Source code
Check.Argu.Para Source code
Class.Score Source code
Display.Warning Source code
Est.Depth Source code
Get.Dels Source code
Get.Order.Div.Overdisp Source code
Get.Overdisp Source code
Get.True.FDR Source code
PS.Est.Depth Man page Source code
PS.FDR Source code
PS.Filter Source code
PS.Main Man page Source code
PS.Sum Source code
Permu.Ind Source code
Quant.Score Source code
Score.Stat Source code
Search.Ord Source code
Trans.Data Source code
dat Man page

Files

MD5
man
man/dat.Rd
man/PS.Est.Depth.Rd
man/PS.Main.Rd
data
data/dat.RData
NAMESPACE
DESCRIPTION
LICENSE
R
R/ps_main.R
R/ps_cmeans.R
R/ps_order.R
R/ps_other.R
R/ps_stat.R
R/ps_rand.R
R/ps_fdr.R
PoissonSeq documentation built on May 19, 2017, 7:34 a.m.

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