Convert an object to a phyloseq object — to_phyloseq • microEDA

S4 generic to convert objects into a phyloseq object. Currently, methods for metaphlanProfile and microEDA objects are implemented.

Usage

to_phyloseq(x, ...)

# S4 method for class 'microEDA'
to_phyloseq(x)

# S4 method for class 'metaphlanProfile'
to_phyloseq(x, metadata = NULL, sample_column = NULL)

Arguments

x: An object of class microEDA.
...: Additional arguments passed to methods (e.g., metadata, sample_column).
metadata: Optional data.frame containing sample metadata.
sample_column: Character string specifying the column in metadata with sample IDs.

Value

An object of class phyloseq.

See also

phyloseq, microEDA, metaphlanProfile-class

Examples

# Convert a microEDA object to phyloseq
data(enterotype, package = "phyloseq")
me <- microEDA(enterotype)
is(me, "microEDA")
#> [1] TRUE
ps <- to_phyloseq(me)
is(ps, "phyloseq")
#> [1] TRUE

# Convert a metaphlanProfile object to phyloseq
mpa <- microEDA::merged_metaphlan_profiles
is(mpa, "metaphlanProfile")
#> [1] TRUE
ps <- to_phyloseq(mpa)
is(ps, "phyloseq")
#> [1] TRUE