setNormalizations: setNormalizations

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

setNormalizations

Description

Set the methods and parameters to compute normalization/scaling factors.

Usage

setNormalizations(
  fun = c("norm_edgeR", "norm_DESeq2", "norm_CSS"),
  method = c("TMM", "poscounts", "CSS")
)

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").

Value

a list object containing the normalization methods and their parameters.

See Also

runNormalizations, norm_edgeR, norm_DESeq2, norm_CSS, norm_TSS

Examples

# Set a TMM normalization
my_TMM_normalization <- setNormalizations(fun = "norm_edgeR", method = "TMM")

# Set some simple normalizations
my_normalizations <- setNormalizations()

# Add a custom normalization
my_normalizations <- c(my_normalizations,
    myNormMethod1 = list("myNormMethod", "parameter1", "parameter2"))

mcalgaro93/benchdamic documentation built on Nov. 28, 2024, 2:16 p.m.