checkNormalization: checkNormalization

In mcalgaro93/benchdamic: Benchmark of differential abundance methods on microbiome data

checkNormalization

Description

Check if the normalization function's name and the method's name to compute normalization/scaling factors are correctly matched.

Usage

checkNormalization(fun, method, ...)

Arguments

fun	a character with the name of normalization function (e.g. "norm_edgeR", "norm_DESeq2", "norm_CSS"...).
method	a character with the normalization method (e.g. "TMM", "upperquartile"... if the fun is "norm_edgeR").
...	other arguments if needed (e.g. for norm_edgeR normalizations).

Value

a list object containing the normalization method and its parameters.

See Also

setNormalizations, norm_edgeR, norm_DESeq2, norm_CSS, norm_TSS

Examples

# Check if TMM normalization belong to "norm_edgeR"
check_TMM_normalization <- checkNormalization(fun = "norm_edgeR",
    method = "TMM")

mcalgaro93/benchdamic documentation built on Sept. 26, 2024, 6:34 p.m.