Import Mothur results as a TreeSummarizedExperiment

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

importMothur(
  assay.file = sharedFile,
  sharedFile,
  taxonomyFile = NULL,
  row.file = taxonomyFile,
  designFile = NULL,
  col.file = designFile
)

Arguments

assay.file

Character scalar. Defines the file path of the feature table to be imported. The File has to be in shared file format as defined in Mothur documentation.

sharedFile

Deprecated. Use assay.file instead.

taxonomyFile

Deprecated. Use row.file instead.

row.file

Character scalar. Defines 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: NULL).

designFile

Deprecated. Use col.file instead.

col.file

Character scalar. Defines file path of the sample metadata to be imported. The File has to be in design file format as defined in Mothur documentation. (Default: NULL).

Value

A TreeSummarizedExperiment object

Details

Results exported from Mothur can be imported as a SummarizedExperiment using importMothur. Except for the assay.file, the other data types, row.file, and col.file, 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/

See also

convertFromPhyloseq convertFromBIOM convertFromDADA2 importQIIME2

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 <- importMothur(assay.file = counts, row.file = taxa, col.file = 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