convert_to {rbiom} | R Documentation |
Convert biom data to an external package class.
Description
Requires the relevant Bioconductor R package to be installed:
convert_to_phyloseq
-convert_to_SE
-convert_to_TSE
-
Usage
convert_to_SE(biom, ...)
convert_to_TSE(biom, ...)
convert_to_phyloseq(biom, ...)
Arguments
biom |
An rbiom object, such as from |
... |
Not Used. |
Details
A SummarizedExperiment object includes counts, metadata, and taxonomy.
phyloseq and TreeSummarizedExperiment additionally includes the tree and sequences.
Value
A phyloseq, SummarizedExperiment, or TreeSummarizedExperiment object.
Examples
## Not run:
library(rbiom)
print(hmp50)
# Requires 'phyloseq', a Bioconductor R package
if (nzchar(system.file(package = "phyloseq"))) {
physeq <- convert_to_phyloseq(hmp50)
print(physeq)
}
# Requires 'SummarizedExperiment', a Bioconductor R package
if (nzchar(system.file(package = "SummarizedExperiment"))) {
se <- convert_to_SE(hmp50)
print(se)
}
# Requires 'TreeSummarizedExperiment', a Bioconductor R package
if (nzchar(system.file(package = "TreeSummarizedExperiment"))) {
tse <- convert_to_TSE(hmp50)
print(tse)
}
## End(Not run)
[Package rbiom version 2.2.1 Index]