validate.list.args {metaseqR} | R Documentation

## Validate list parameters for several metaseqR functions

### Description

This function validates the arguments passed by the user to the normalization, statistics and filtering algorithms supported by metaseqR. As these are given into lists and passed to the algorithms, the list member names must be valid algorithm arguments for the pipeline not to crash. This function performs these checks and ignores any invalid arguments.

### Usage

        validate.list.args(what, method = NULL, arg.list)

### Arguments

`what` | what a keyword determining the procedure for which to validate arguments. It can be one of `"normalization"`, `"statistics"`, `"gene.filter"`, `"exon.filter"` or `"biotype.filter"`.
`method` | the normalization/statistics/filtering algorithm included in metaseqR for which to validate user input. 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).
`arg.list` | the user input list of arguments.

### Value

A list with valid arguments to be used as user input in the algorithms supported by metaseqR.

### Author(s)

Panagiotis Moulos

### Examples

    norm.args.edger <- list(method="TMM",refColumn=NULL,
        logratioTrim=0.3,sumTrim=0.05,doWeighting=TRUE,
        Bcutoff=-1e10,p=0.75)
    # Bcutoff does not exist, will throw a warning and ignore it.
    norm.args.edger <- validate.list.args("normalization",
        "edger",norm.args.edger)

[Package metaseqR version 1.20.0 Index]