norm_TSS | R Documentation |
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.
norm_TSS(object, assay_name = "counts", method = "TSS", verbose = TRUE)
object |
a phyloseq or TreeSummarizedExperiment object. |
assay_name |
the name of the assay to extract from the
TreeSummarizedExperiment object (default |
method |
normalization method to be used. |
verbose |
an optional logical value. If |
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.
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_TSS(object = ps) # The phyloseq object now contains the scaling factors: scaleFacts <- phyloseq::sample_data(ps_NF)[, "NF.TSS"] head(scaleFacts)
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