getDefaults: Default parameters for several metaseqr functions

In pmoulos/metaseqR2-local: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Default parameters for several metaseqr functions

Description

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.

Usage

    getDefaults(what, method = NULL)

Arguments

what	a keyword determining the procedure for which to fetch the default settings according to method parameter. It can be one of "normalization", "statistics", "geneFilter", "exonFilter" or "biotypeFilter".
method	the supported algorithm included in metaseqR for which to fetch the default settings. Se Details.

Details

When what is "normalization", method is one of "edaseq", "deseq", "edger", "noiseq" or "nbpseq". When what is "statistics", method is one of "deseq", "edger", "noiseq", "limma", or "nbpseq". When method is "biotypeFilter", what is the input organism (see the main metaseqr2 help page for a list of supported organisms).

Value

A list with default setting that can be used directly in the call of metaseqr.

Author(s)

Panagiotis Moulos

Examples

normArgsEdaseq <- getDefaults("normalization","edaseq")
statArgsEdger <- getDefaults("statistics","edger")

pmoulos/metaseqR2-local documentation built on May 21, 2024, 3:46 a.m.