runNormalizations {benchdamic} | R Documentation |
Add normalization/scaling factors to a phyloseq object
runNormalizations(normalization_list, object, verbose = TRUE)
normalization_list |
a list object containing the normalization methods and their parameters. |
object |
a phyloseq object. |
verbose |
an optional logical value. If |
A phyloseq object containing the normalization/scaling factors.
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)