countsTable


A subset of simulated data. It is used as an example for running some 
functions in this package.


The purpose of this package is to discover the genes that
are differentially expressed between two conditions in RNA-seq
experiments. Gene expression is measured in counts of
transcripts and modeled with the Negative Binomial (NB)
distribution using a shrinkage approach for dispersion
estimation. The method of moment (MM) estimates for dispersion
are shrunk towards an estimated target, which minimizes the
average squared difference between the shrinkage estimates and
the initial estimates. The exact per-gene probability under the
NB model is calculated, and used to test the hypothesis that
the expected expression of a gene in two conditions identically
follow a NB distribution.

Danni Yu

sSeq

Shrinkage estimation of dispersion in Negative Binomial models
for RNA-seq experiments with small sample size

countsTable function

The format is:
 num [1:10000, 1:2] 90 155 13347 254 228 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:10000] "1_FALSE" "2_FALSE" "3_TRUE" "4_FALSE" ...
  ..$ : chr [1:2] "A1" "B1"

Format

A subset of simulated data. It is used as an example for running some 
functions in this package.

countsTable: An Example Simulation Data

Description

Usage

Arguments

Format

Details

Examples