norm_TSS {benchdamic}

R Documentation

norm_TSS

Description

Calculate the raw library sizes from a phyloseq object. If used to divide counts, known as Total Sum Scaling normalization (TSS).

Usage

norm_TSS(object, method = "TSS", verbose = TRUE)

Arguments

object	phyloseq object containing the counts to be normalized.
method	normalization method to be used.
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 TSS scaling factors is added to the phyloseq sample_data slot.

See Also

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_TSS(object = ps)
# The phyloseq object now contains the scaling factors:
scaleFacts <- phyloseq::sample_data(ps_NF)[, "NF.TSS"]
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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