loadFromMothur {mia} | R Documentation |
SummarizedExperiment
This method creates a SummarizedExperiment
object from Mothur
files provided as input.
loadFromMothur(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 loadFromMothur
. Except for the
sharedFile
, the other data types, taxonomyFile
, and
designFile
, are optional, but are highly encouraged to be provided.
A
SummarizedExperiment
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/
makeTreeSummarizedExperimentFromphyloseq
makeSummarizedExperimentFromBiom
makeTreeSummarizedExperimentFromDADA2
loadFromQIIME2
# 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