norm_CSS {benchdamic}

R Documentation

norm_CSS

Description

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.

Usage

norm_CSS(object, method = "default", verbose = TRUE)

Arguments

object	phyloseq object containing the counts to be normalized.
method	normalization scaling parameter (default method = "default"). If "median", the median of the normalization factors is used as scaling (Paulson et al. 2013).
verbose	an optional logical value. If TRUE, information about the steps of the algorithm is printed. Default verbose = TRUE.

Value

A new column containing the CSS scaling factors is added to the phyloseq sample_data slot.

See Also

calcNormFactors for details. setNormalizations and runNormalizations to fastly set and run normalizations.

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))

# 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)))

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