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

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