norm_CSS: norm_CSS

In mcalgaro93/benchdamic: Benchmark of differential abundance methods on microbiome data

norm_CSS

Description

Calculate normalization factors from a phyloseq or TreeSummarizedExperiment object. Inherited from metagenomeSeq calcNormFactors function which performs the Cumulative Sum Scaling normalization.

Usage

norm_CSS(object, assay_name = "counts", method = "CSS", verbose = TRUE)

Arguments

object	a phyloseq or TreeSummarizedExperiment object.
assay_name	the name of the assay to extract from the TreeSummarizedExperiment object (default assayName = "counts"). Not used if the input object is a phyloseq.
method	normalization method to be used (only CSS).
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 normalization factors is added to the sample_data slot of the phyloseq object or the colData slot of the TreeSummarizedExperiment object.

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 normalization factors
ps_NF <- norm_CSS(object = ps, method = "CSS")
# The phyloseq object now contains the normalization factors:
CSSFacts <- phyloseq::sample_data(ps_NF)[, "NF.CSS"]
head(CSSFacts)

# VERY IMPORTANT: metagenomeSeq uses scaling factors to normalize counts 
# (even though they are called normalization factors). These factors are used
# internally by a regression model. To make CSS size factors available for 
# edgeR, we need to transform them into normalization factors. This is 
# possible by dividing the factors for the library sizes and renormalizing. 
normCSSFacts = CSSFacts / colSums(phyloseq::otu_table(ps_stool_16S))
# Renormalize: multiply to 1
normFacts = normCSSFacts/exp(colMeans(log(normCSSFacts)))

mcalgaro93/benchdamic documentation built on March 10, 2024, 10:40 p.m.