importMothur | R Documentation |
TreeSummarizedExperiment
This method creates a TreeSummarizedExperiment
object from Mothur
files provided as input.
importMothur(sharedFile, taxonomyFile = NULL, designFile = NULL)
sharedFile |
a single |
taxonomyFile |
a single |
designFile |
a single |
Results exported from Mothur can be imported as a
SummarizedExperiment
using importMothur
. Except for the
sharedFile
, the other data types, taxonomyFile
, and
designFile
, are optional, but are highly encouraged to be provided.
A
TreeSummarizedExperiment
object
Leo Lahti and Tuomas Borman. Contact: microbiome.github.io
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/
makeTreeSEFromPhyloseq
makeTreeSEFromBiom
makeTreeSEFromDADA2
importQIIME2
# 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(counts, taxa, meta)
# Convert SE to TreeSE
tse <- as(se, "TreeSummarizedExperiment")
tse
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