metaseqR (version 1.12.2)

validate.alg.args: Validate normalization and statistical algorithm arguments

Description

This function checks and validates the arguments passed by the user to the normalization and statistics algorithms supported by metaseqR. As these are given into lists and passed to the algorithms, the list members must be checked for NULL, valid names etc. This function performs these checks and ignores any invalid arguments.

Usage

validate.alg.args(normalization, statistics, 
        norm.args, stat.args)

Arguments

normalization

a keyword determining the normalization strategy to be performed by metaseqR. See metaseqr main help page for details.

statistics

the statistical tests to be performed by metaseqR. See metaseqr main help page for details.

norm.args

the user input list of normalization arguments. See metaseqr main help page for details.

stat.args

the user input list of statistical test arguments. See metaseqr main help page for details.

Value

• A list with two members (norm.args, stat.args) with valid arguments to be used as user input for the algorithms supported by metaseqR.

Examples

normalization <- "edaseq"
statistics <- "edger"
norm.args <- get.defaults("normalization","edaseq")
stat.args <- get.defaults("statistics","deseq")
# Will return as is
val <- validate.alg.args(normalization,statistics,norm.args,stat.args)
val$norm.args
val$stat.args
# but...
stat.args <- c(stat.args,my.irrelevant.arg=999)
val <- validate.alg.args(normalization,statistics,norm.args,stat.args)
# irrelevant argument will be removed
val$norm.args
val$stat.args