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ABSSeq (version 1.2.0)

ABSSeq: a new RNA-Seq analysis method based on absolute expression differences and generalized Poisson model

Description

Inferring differential expression genes by absolute expression differences between two groups, utilizing generalized Poisson model to account for over-dispersion across samples and heterogeneity of differential expression across genes.

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Version

1.2.0

License

GPL (>= 3)

Maintainer

Wentao Yang

Last Published

February 15th, 2017

Functions in ABSSeq (1.2.0)

estimateSizeFactorsForMatrix

Low-level function to estimate size factors with robust regression.

counts

Accessors for the 'counts' slot of a ABSDataSet object.

plotDifftoBase

Plot absolute differencs

results

Accessor functions for the result from a ABSDataSet

sizeFactors

Accessors for the 'sizeFactor' slot of a ABSDataSet object.

simuN5

Simulated study with random outliers

normalFactors

Estimating size factors from the reads count table

normMethod

Accessors for the 'normMethod' slot of a ABSDataSet object.

groups

Accessors for the 'groups' slot of a ABSDataSet object.

GPTest

Testing the differential expression

ABSDataSet

ABSDataSet object and constructors

calPara

Calculate parameters for generalized Poisson test (GPTest)

SumInfo

An S4 class that stores a string.