DSS.DE

A matrix of integers with rows corresponding to
    genes and columns for samples.

counts

A vector representing the treatment groups. It must be
	a vector of 0 and 1. The length of the vector must match the number
	of columns of input count matrix.

design


  This is the top level wrapper function for RNA-seq differential expression
  analysis in a two-group comparison. Users only need to provide the
  count matrix and a vector for design, and obtain DE test results. 


DSS is an R library performing differntial analysis for
count-based sequencing data. It detectes differentially
expressed genes (DEGs) from RNA-seq, and differentially
methylated loci or regions (DML/DMRs) from bisulfite sequencing
(BS-seq). The core of DSS is a new dispersion shrinkage method
for estimating the dispersion parameter from Gamma-Poisson or
Beta-Binomial distributions.

Hao Wu

Dispersion shrinakge for sequencing data.

DSS.DE function

This is the top level wrapper function for RNA-seq differential expression
  analysis in a two-group comparison. Users only need to provide the
  count matrix and a vector for design, and obtain DE test results.

Perform RNA-seq differential expression analysis in two-group comparison

index for input gene orders, integers from 1 to the
    number of genes.

gene Index

sample mean (after normalization) for sample A.

sample mean (after normalization) for sample B.

log fold change of expressions between two groups.

differences in expressions between two groups.

difExpr

stats

pval

input gene annotations supplied as AnnotatedDataFrame
    when constructed the SeqCountData object.

DSS.DE: Perform RNA-seq differential expression analysis in two-group comparison

Description

Usage

Arguments

Value

Examples