norm_CSS {benchdamic} | R Documentation |
Calculate scaling factors from a phyloseq object to scale the raw library sizes. Inherited from metagenomeSeq 'calcNormFactors' function which performs the Cumulative Sum Scaling normalization.
norm_CSS(object, method = "default", verbose = TRUE)
object |
phyloseq object containing the counts to be normalized. |
method |
normalization scaling parameter (default
|
verbose |
an optional logical value. If |
A new column containing the CSS scaling factors is added to the
phyloseq sample_data
slot.
calcNormFactors
for details.
setNormalizations
and runNormalizations
to fastly
set and run normalizations.
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)) # Calculate the scaling factors ps_NF <- norm_CSS(object = ps, method = "median") # The phyloseq object now contains the scaling factors: scaleFacts <- phyloseq::sample_data(ps_NF)[, "NF.CSSmedian"] head(scaleFacts) # VERY IMPORTANT: to convert scaling factors to normalization factors # multiply them by the library sizes and renormalize. normFacts = scaleFacts * phyloseq::sample_sums(ps_stool_16S) # Renormalize: multiply to 1 normFacts = normFacts/exp(colMeans(log(normFacts)))