get.defaults

a keyword determining the procedure for which
    to fetch the default settings according to method
    parameter. It can be one of <code>"normalization"</code>,
    <code>"statistics"</code>, <code>"gene.filter"</code>,
    <code>"exon.filter"</code> or <code>"biotype.filter"</code>.

what

the supported algorithm included in
    metaseqR for which to fetch the default settings. When
    <code>what</code> is <code>"normalization"</code>, method is one of
    <code>"edaseq"</code>, <code>"deseq"</code>, <code>"edger"</code>,
    <code>"noiseq"</code> or <code>"nbpseq"</code>. When <code>what</code> is
    <code>"statistics"</code>, method is one of <code>"deseq"</code>,
    <code>"edger"</code>, <code>"noiseq"</code>, <code>"bayseq"</code>,
    <code>"limma"</code> or <code>"nbpseq"</code>. When <code>method</code> is
    <code>"biotype.filter"</code>, <code>what</code> is the input
    organism (see the main <code><a href="/link/metaseqr?package=metaseqR&version=1.12.2" rd-options="" data-mini-rdoc="metaseqR::metaseqr">metaseqr</a></code> help page
    for a list of supported organisms).

method

This function returns a list with the default settings
    for each filtering, statistical and normalization
    algorithm included in the metaseqR package. See the
    documentation of the main function and the documentation
    of each statistical and normalization method for details.

Provides an interface to several normalization and
    statistical testing packages for RNA-Seq gene expression data.
    Additionally, it creates several diagnostic plots, performs
    meta-analysis by combinining the results of several statistical
    tests and reports the results in an interactive way.

Panagiotis Moulos

metaseqR

An R package for the analysis and result reporting
    of RNA-Seq data by combining multiple statistical
    algorithms.

get.defaults function

the supported algorithm included in
    metaseqR for which to fetch the default settings. When
    <code>what</code> is <code>"normalization"</code>, method is one of
    <code>"edaseq"</code>, <code>"deseq"</code>, <code>"edger"</code>,
    <code>"noiseq"</code> or <code>"nbpseq"</code>. When <code>what</code> is
    <code>"statistics"</code>, method is one of <code>"deseq"</code>,
    <code>"edger"</code>, <code>"noiseq"</code>, <code>"bayseq"</code>,
    <code>"limma"</code> or <code>"nbpseq"</code>. When <code>method</code> is
    <code>"biotype.filter"</code>, <code>what</code> is the input
    organism (see the main <code><a href="metaseqr" rd-options="">metaseqr</a></code> help page
    for a list of supported organisms).

get.defaults: Default parameters for several metaseqr functions

Description

Usage

Arguments

Value

Examples