loadFromMothur {mia} | R Documentation

## Import Mothur results as a `SummarizedExperiment`

### Description

This method creates a `SummarizedExperiment` object from `Mothur` files provided as input.

### Usage

    loadFromMothur(sharedFile, taxonomyFile = NULL, designFile = NULL)

### Arguments

`sharedFile` | a single `character` value defining the file path of the feature table to be imported. The File has to be in `shared file` format as defined in Mothur documentation.
`taxonomyFile` | a single `character` value defining the file path of the taxonomy table to be imported. The File has to be in `taxonomy file` or `constaxonomy file` format as defined in Mothur documentation. (default: `taxonomyFile = NULL`).
`designFile` | a single `character` value defining the file path of the sample metadata to be imported. The File has to be in `desing file` format as defined in Mothur documentation. (default: `designFile = NULL`).

### Details

Results exported from Mothur can be imported as a `SummarizedExperiment` using `loadFromMothur`. Except for the `sharedFile`, the other data types, `taxonomyFile`, and `designFile`, are optional, but are highly encouraged to be provided.

### Value

A `SummarizedExperiment` object

### Author(s)

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

### References

https://mothur.org/ https://mothur.org/wiki/shared_file/ https://mothur.org/wiki/taxonomy_file/ https://mothur.org/wiki/constaxonomy_file/ https://mothur.org/wiki/design_file/

### See Also

`makeTreeSummarizedExperimentFromPhyloseq` `makeSummarizedExperimentFromBiom` `makeTreeSummarizedExperimentFromDADA2` `loadFromQIIME2`

### Examples

    # Abundance table
    counts <- system.file("extdata", "mothur_example.shared", package = "mia")
    # Taxa table (in "cons.taxonomy" or "taxonomy" format)
    taxa <- system.file("extdata", "mothur_example.cons.taxonomy", package = "mia")
    #taxa <- system.file("extdata", "mothur_example.taxonomy", package = "mia")
    # Sample meta data
    meta <- system.file("extdata", "mothur_example.design", package = "mia")

    # Creates se object from files
    se <- loadFromMothur(counts, taxa, meta)
    se

[Package mia version 1.2.7 Index]