Import Mothur results as a TreeSummarizedExperiment

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

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).

Value

A TreeSummarizedExperiment

object

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.

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/

Author

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

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)
# Convert SE to TreeSE
tse <- as(se, "TreeSummarizedExperiment")
tse
#> class: TreeSummarizedExperiment 
#> dim: 100 100 
#> metadata(0):
#> assays(1): counts
#> rownames(100): Otu001 Otu002 ... Otu099 Otu100
#> rowData names(8): OTU Size ... Family Genus
#> colnames(100): Sample1 Sample2 ... Sample99 Sample100
#> colData names(7): group sex ... numOtus Group
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: NULL
#> rowTree: NULL
#> colLinks: NULL
#> colTree: NULL

Import Mothur results as a `TreeSummarizedExperiment`