makePhyloseqFromTreeSummarizedExperiment {mia} | R Documentation |
This function creates a phyloseq object from a TreeSummarizedExperiment
object. By using abund_values
, it is possible to specify which table
from assay
is added to the phyloseq object.
makePhyloseqFromTreeSummarizedExperiment(x, ...) ## S4 method for signature 'SummarizedExperiment' makePhyloseqFromTreeSummarizedExperiment(x, abund_values = "counts") ## S4 method for signature 'TreeSummarizedExperiment' makePhyloseqFromTreeSummarizedExperiment(x, ...)
x |
a |
... |
additional arguments |
abund_values |
A single character value for selecting the
|
makePhyloseqFromTreeSummarizedExperiment
is used for creating a
phyloseq object from TreeSummarizedExperiment object.
An object of class Phyloseq
object.
Leo Lahti and Tuomas Borman. Contact: microbiome.github.io
# Get tse object data(GlobalPatterns) tse <- GlobalPatterns # Create a phyloseq object from it phy <- makePhyloseqFromTreeSummarizedExperiment(tse) phy # By default the chosen table is counts, but if there are other tables, # they can be chosen with abund_values. # Counts relative abundances table tse <- transformCounts(tse, method = "relabundance") phy2 <- makePhyloseqFromTreeSummarizedExperiment(tse, abund_values = "relabundance") phy2