makePhyloseqFromTreeSummarizedExperiment {mia} | R Documentation

## Create a phyloseq object from a TreeSummarizedExperiment object

### Description

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.

### Usage

    makePhyloseqFromTreeSummarizedExperiment(x, ...)

    ## S4 method for signature 'SummarizedExperiment'
    makePhyloseqFromTreeSummarizedExperiment(x, abund_values = "counts")

    ## S4 method for signature 'TreeSummarizedExperiment'
    makePhyloseqFromTreeSummarizedExperiment(x, ...)

### Arguments

`x` | a `TreeSummarizedExperiment` object
`...` | additional arguments
`abund_values` | A single character value for selecting the `assay` to be included in the phyloseq object that is created. By default, it is counts table.

### Details

`makePhyloseqFromTreeSummarizedExperiment` is used for creating a phyloseq object from TreeSummarizedExperiment object.

### Value

An object of class `Phyloseq` object.

### Author(s)

Leo Lahti and Tuomas Borman. Contact: microbiome.github.io

### Examples

    # 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

[Package mia version 1.2.7 Index]