norm_TSS: norm_TSS

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

norm_TSS

Description

Calculate the Total Sum Scaling (TSS) factors for a phyloseq or a TreeSummarizedExperiment object, i.e. the library sizes. If the counts are divided by the scaling factors, a relative abundance is obtained.

Usage

norm_TSS(object, assay_name = "counts", method = "TSS", 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.
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 sample_data slot of the phyloseq object or the colData slot of the TreeSummarizedExperiment object.

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)

mcalgaro93/benchdamic documentation built on Nov. 28, 2024, 2:16 p.m.