runNormalizations {benchdamic} | R Documentation

## runNormalizations

### Description

Add normalization/scaling factors to a phyloseq object

### Usage

    runNormalizations(normalization_list, object, verbose = TRUE)

### Arguments

`normalization_list` | a list object containing the normalization methods and their parameters.
`object` | a phyloseq object.
`verbose` | an optional logical value. If `TRUE`, information about the steps of the algorithm is printed. Default `verbose = TRUE`.

### Value

A phyloseq object containing the normalization/scaling factors.

### See Also

`setNormalizations`

### Examples

    set.seed(1)
    # Create a very simple phyloseq object
    counts <- matrix(rnbinom(n = 60, size = 3, prob = 0.5), nrow = 10, ncol = 6)
    metadata <- data.frame("Sample" = c("S1", "S2", "S3", "S4", "S5", "S6"),
                           "group" = as.factor(c("A", "A", "A", "B", "B", "B")))
    ps <- phyloseq::phyloseq(phyloseq::otu_table(counts, taxa_are_rows = TRUE),
                             phyloseq::sample_data(metadata))

    # Set some simple normalizations
    my_normalizations <- setNormalizations()

    # Add them to the phyloseq object
    ps <- runNormalizations(normalization_list = my_normalizations, object = ps)

[Package benchdamic version 1.0.0 Index]