Create a phyloseq object from a TreeSummarizedExperiment object

Source: R/convertToPhyloseq.R

Create a phyloseq object from a TreeSummarizedExperiment object

convertToPhyloseq(x, ...)

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

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

Arguments

x

a TreeSummarizedExperiment object

...

Additional arguments. Not used currently.

assay.type

Character scalar. Specifies the name of assay used. (Default: "counts")

assay_name

Deprecated. Use assay.type instead.

tree.name

Character scalar. Specifies the name of the tree to be included in the phyloseq object that is created, (Default: "phylo")

tree_name

Deprecated. Use tree.name instead.

Value

convertToPhyloseq returns an object of class phyloseq

Details

convertToPhyloseq 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.

Author

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

Examples


### Coerce a TreeSE object to a phyloseq object
# Get tse object
data(GlobalPatterns)
tse <- GlobalPatterns

# Create a phyloseq object from it
phy <- convertToPhyloseq(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 <- convertToPhyloseq(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 ]