dexus.parallel

Either a vector of counts or a raw data matrix,
  where columns are interpreted as samples and rows as
  genomic regions.

The number of cores (CPUs) that will be
  used by the parallelization.

ncores

Normalization method to be used.
  (Default="RLE")

normalization

A transcript is
  considered as not expressed if all counts are smaller
  than the given value. (Default=1)

ignoreIfAllCountsSmaller

Type of the result object; can either
  be a list ("list") or an instance of "DEXUSResult"
  ("S4"). (Default="S4").

resultObject

Other options to be passed to <code>dexus()</code>.


  Speeds up DEXUS by using multiple processors. Uses the
  <code>parallel</code> package to parallelize a DEXUS call.


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

dexus.parallel function

Speeds up DEXUS by using multiple processors. Uses the
  <code>parallel</code> package to parallelize a DEXUS call.

dexus.parallel: A parallel version of DEXUS.

Description

Usage

Arguments

Value

Examples