Create a phyloseq object from a TreeSummarizedExperiment object

This function creates a phyloseq object from a TreeSummarizedExperiment object. By using assay.type, it is possible to specify which table from assay is added to the phyloseq object.

makePhyloseqFromTreeSE(x, ...)

# S4 method for SummarizedExperiment
makePhyloseqFromTreeSE(x, assay.type = "counts", assay_name = NULL, ...)

# S4 method for TreeSummarizedExperiment
makePhyloseqFromTreeSE(x, tree.name = tree_name, tree_name = "phylo", ...)

makePhyloseqFromTreeSummarizedExperiment(x, ...)

# S4 method for ANY
makePhyloseqFromTreeSummarizedExperiment(x, ...)

Arguments

x: a TreeSummarizedExperiment object
...: additional arguments
assay.type: A single character value for selecting the assay to be included in the phyloseq object that is created. (By default: assay.type = "counts")
assay_name: a single character value for specifying which assay to use for calculation. (Please use assay.type instead. At some point assay_name will be disabled.)
tree.name: a single character value for specifying which tree will be included in the phyloseq object that is created, (By default: tree.name = "phylo")
tree_name: Deprecated. Use tree.name instead.

Value

An object of class Phyloseq object.

Details

makePhyloseqFromTreeSE is used for creating a phyloseq object from TreeSummarizedExperiment object.

Author

Leo Lahti and Tuomas Borman. Contact: microbiome.github.io

Examples

# Get tse object
data(GlobalPatterns)
tse <- GlobalPatterns

# Create a phyloseq object from it
phy <- makePhyloseqFromTreeSE(tse)
phy
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 19216 taxa and 26 samples ]
#> sample_data() Sample Data:       [ 26 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 19216 taxa by 7 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 19216 tips and 19215 internal nodes ]

# By default the chosen table is counts, but if there are other tables,
# they can be chosen with assay.type.

# Counts relative abundances table
tse <- transformAssay(tse, method = "relabundance")
phy2 <- makePhyloseqFromTreeSE(tse, assay.type = "relabundance")
phy2
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 19216 taxa and 26 samples ]
#> sample_data() Sample Data:       [ 26 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 19216 taxa by 7 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 19216 tips and 19215 internal nodes ]