View source: R/convertFromPhyloseq.R
convertFromPhyloseq | R Documentation |
TreeSummarizedExperiment
object from a phyloseq objectCreate a TreeSummarizedExperiment
object from a phyloseq object
Create a phyloseq object from a TreeSummarizedExperiment
object
convertFromPhyloseq(x)
convertToPhyloseq(x, ...)
## S4 method for signature 'SummarizedExperiment'
convertToPhyloseq(x, assay.type = "counts", assay_name = NULL, ...)
## S4 method for signature 'TreeSummarizedExperiment'
convertToPhyloseq(x, tree.name = tree_name, tree_name = "phylo", ...)
x |
a
|
... |
Additional arguments. Not used currently. |
assay.type |
|
assay_name |
Deprecated. Use |
tree.name |
|
tree_name |
Deprecated. Use |
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.
convertFromPhyloseq
returns an object of class
TreeSummarizedExperiment
convertToPhyloseq
returns an object of class
phyloseq
### 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)
}
### 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
# 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
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