edgeR.QL.running: Implement Quasi likelihood method by default settings.

In lunge111/intSEQ: Differential Expression Analysis of RNA-seq Data with Integrated Likelihood Method

Description

See detail for default options.

Usage

edgeR.QL.running(count.data, cond, normalize= TRUE)

Arguments

count.data	A numeric matrix of the count table.
cond	A vector of factors or numeric of the predictor variable.
normalize	Logical, whether to use "TMM" normalization.

Details

The default method of normalization is "TMM" using the calcNormFactors in edgeR. Estimation of dispersion parameters uses estimateDisp function with default options. Then glmQLFit and glmQLFTest are called with defaults.

Value

An object of class DGEGLM.

Author(s)

Yilun Zhang, David Rocke

References

McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297

Examples

data(count.data)
data(condition)
pv.quasi <- edgeR.QL.running(count.data,condition)

lunge111/intSEQ documentation built on May 20, 2019, 9:38 a.m.