setNormalizations {benchdamic} | R Documentation

## setNormalizations

### Description

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

### Usage

    setNormalizations(
      fun = c("norm_edgeR", "norm_DESeq2", "norm_CSS", "norm_edgeR"),
      method = c("TMM", "poscounts", "median", "none")
    )

### 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"))

[Package benchdamic version 1.0.0 Index]