metaseqR (version 1.12.2)

validate.list.args: 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.

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)