`[`,DEXUSResult,character-method

`[`,DEXUSResult,logical-method

`[`,DEXUSResult,numeric-method

Either a numeric vector of indices or a
  character vector containing the transcript names.


  Information about specific transcripts can be accessed in
  the "DEXUSResult" object by using the standard brackets
  "[idx]" for subsetting. Either transcript names or
  transcript indices can be used.


DEXUS identifies differentially expressed genes in RNA-Seq
data under all possible study designs such as studies without
replicates, without sample groups, and with unknown conditions.
DEXUS works also for known conditions, for example for RNA-Seq
data with two or multiple conditions. RNA-Seq read count data
can be provided both by the S4 class Count Data Set and by read
count matrices. Differentially expressed transcripts can be
visualized by heatmaps, in which unknown conditions,
replicates, and samples groups are also indicated. This
software is fast since the core algorithm is written in C. For
very large data sets, a parallel version of DEXUS is provided
in this package. DEXUS is a statistical model that is selected
in a Bayesian framework by an EM algorithm. DEXUS does not need
replicates to detect differentially expressed transcripts,
since the replicates (or conditions) are estimated by the EM
method for each transcript. The method provides an
informative/non-informative value to extract differentially
expressed transcripts at a desired significance level or power.

Guenter Klambauer

dexus

DEXUS - Identifying Differential Expression in RNA-Seq Studies
with Unknown Conditions or without Replicates

`[` function

Information about specific transcripts can be accessed in
  the "DEXUSResult" object by using the standard brackets
  "[idx]" for subsetting. Either transcript names or
  transcript indices can be used.

`[`: Subsetting a "DEXUSResult".

Description

Arguments

Value

Examples