get.defaults {metaseqR} | R Documentation

## 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

        get.defaults(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"`, `"gene.filter"`, `"exon.filter"` or `"biotype.filter"`.
`method` | the supported algorithm included in metaseqR for which to fetch the default settings. 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"`, `"bayseq"`, `"limma"` or `"nbpseq"`. When `method` is `"biotype.filter"`, `what` is the input organism (see the main `metaseqr` 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

    norm.args.edaseq <- get.defaults("normalization","edaseq")
    stat.args.edger <- get.defaults("statistics","edger")

[Package metaseqR version 1.27.13 Index]