Create a TreeSummarizedExperiment object from a phyloseq object

Create a TreeSummarizedExperiment object from a phyloseq object

Create a phyloseq object from a TreeSummarizedExperiment object

convertFromPhyloseq(x)

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

convertFromPhyloseq returns an object of class TreeSummarizedExperiment

convertToPhyloseq returns an object of class phyloseq

Details

convertFromPhyloseq converts phyloseq objects into TreeSummarizedExperiment objects. All data stored in a phyloseq object is transferred.

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.

Examples

### Coerce a phyloseq object to a TreeSE object
if (requireNamespace("phyloseq")) {
    data(GlobalPatterns, package="phyloseq")
    convertFromPhyloseq(GlobalPatterns)
    data(enterotype, package="phyloseq")
    convertFromPhyloseq(enterotype)
    data(esophagus, package="phyloseq")
    convertFromPhyloseq(esophagus)
}
#> Loading required namespace: phyloseq
#> class: TreeSummarizedExperiment 
#> dim: 58 3 
#> metadata(0):
#> assays(1): counts
#> rownames(58): 59_8_22 59_5_13 ... 65_9_9 59_2_6
#> rowData names(0):
#> colnames(3): B C D
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (58 rows)
#> rowTree: 1 phylo tree(s) (58 leaves)
#> colLinks: NULL
#> colTree: NULL

### 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 ]